|
| Status |
Public on Apr 14, 2023 |
| Title |
LentiAS 1 [Hi-C] |
| Sample type |
SRA |
| |
|
| Source name |
Primary rat Schwann cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: sciatic nerve
cell type: Schwann cells
treatment: infected/treated with virus that will overexpress the Egr2-AS-RNA
|
| Treatment protocol |
Overexpression of the Egr2-AS-RNA (and the backbone virus control carrying GFP) was performed with a lentiviral construct at a concentration of 2UFC/cell, with polybrene at a 1:1500 concentration, for 48 hours. The virus generation was described in detail in previous work (Martinez-Moreno et al., 2017). The plasmid to generate the lentivirus was deposited to Addgene and is available to order (#177737).
|
| Growth protocol |
Cells were cultured in DMEM supplemented with 10% FBS, 4 μM forskolin, 5 ng/ml heregulin-β1 and antibiotics, in surface modified 75cc Primaria flasks. Cells were fed every other day and passaged at 80% confluence.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HiC was performed using the Arima-HiC kit. As per their protocol, we tested the amount of input sample beforehand and we used 2 million cells per each independent sample. We did QC on samples in every recommended step. Sonication was performed using the Covaris s220 instrument to a fragment size of 300-400bp (Settings: Power: 5, Duty Factor: 10%, Cycles per Burst: 200, and Time: 60 sec per process). We used KAPA Hyper Prep Kit to generate libraries. The primers used for indexing were obtained from Illumina, and the libraries were quantified and QC was done using the KAPA Library Quantification Kit. Libraries were sequenced by GENEWIZ using the Illumina HiSeq 2500 system to acquire 150 bp paired-end sequence reads, reaching 300M reads for each sample based on total usable reads >20Kb.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
LentiAS2
|
| Data processing |
Contact matrices were generated on the Rnor6.0/rn6 version of the Rattus norvegicus genome assembly (https://hgdownload.soe.ucsc.edu/goldenPath/rn6/bigZips/rn6.fa.gz) using HiC-Pro (https://github.com/nservant/HiC-Pro).
Contact matrix .matrix files are in standard triple sparse format (https://nservant.github.io/HiC-Pro/RESULTS.html), which has three columns: The first two columns show the indices of the interacting chromosomal locations (see below for description); the third column shows the read count
The genomic coordinates of each index in the first two columns of the .matrix files can be found in the matching .bed files.
When necessary, .hic files were prepared from the .matrix files (and their corresponding .bed files) using the hicdc2hic routine of the HiCDCPlus Bioconductor package.
Genome build: Rn6 (Rnor_6.0)
|
| |
|
| Submission date |
Apr 26, 2022 |
| Last update date |
Apr 15, 2023 |
| Contact name |
Jorge Eduardo Fajardo |
| E-mail(s) |
eduardo@fiserlab.org
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Systems and Computational Biology
|
| Street address |
1300 Morris Park Avenue
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE201625 |
Egr2 promoter antisense RNA as coordinator of chromatin remodeling and genome reorganization in Schwann cells [Hi-C] |
| GSE201627 |
Egr2 promoter antisense RNA as coordinator of chromatin remodeling and genome reorganization in Schwann cells |
|
| Relations |
| BioSample |
SAMN27861646 |
| SRA |
SRX15010739 |
