|
| Status |
Public on Nov 10, 2020 |
| Title |
ChIP_INPUT_R61_R2_3 |
| Sample type |
SRA |
| |
|
| Source name |
Mice hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain: CBA x C57BL/6 (50% CBA & 50% C57BL6)
genotype/variation: R6/1
tissue: hippocampal tissue
age: 30-week-old mice
chip antibody: NA
|
| Treatment protocol |
Frozen hippocampal tissue from WT and R6/1 mice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq: Frozen hippocampus from 5 mice were pooled together, homogenized in PBS supplemented with proteinase inhibitors and posteriorly cross-linked with formaldehyde 1% for 15 minutes at r. t. Cross-linking reaction was stopped by a 5 minutes incubation with 2 M glycine and the cross-linked material was washed 3 times with ice-cold PBS. Cells were lysed and nuclei were extracted using nuclei extraction buffer. Purified nuclear fraction was subjected to sonication using Bioruptor Pico (Diagenode) to obtain DNA fragments of 200-500 bp. Sonicated chromatin was incubated with anti-rabbit magnetic bead pre-complexed with 10 µg of α-lamin B1 antibody O/N at 4 ºC. After 6 washes with RIPA buffer, chromatin was eluted and de-crosslinked by O/N incubation at 65 ºC, followed by a 30 minutes RNAse and 2 hours Proteinase K treatments. DNA purification was carried out with MinElute PCR Purification KIT and libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit from Illumina according to the manufacturer’s instructions. DNA size selection was performed after PCR amplification using E-Gel Precast Agarose Electrophoresis System. Samples were sequenced single-end using 50 bp reads on the Hi-Seq 4000 platforms. For each biological replicate (R1, R2 and R3), three samples corresponding to their respective sequencing lane are provided.
Libraries were prepared according to Illumina instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ChIP-seq experiment
|
| Data processing |
Sequence reads of the samples were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1. All the replicates of the same condition were pooled in a single file.
Genome-wide profiles in BedGraph format are the subtraction of Input samples from the LB1 pool of experiments
Domain detection of the LB1 pool against the INPUT pool at WT and R6/1 conditions were performed with EDD (PubMed ID 24782521). Peaks were reported in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/ATAC-seq)
Files *.bed (BED, ChIP-seq signal enriched regions)
|
| |
|
| Submission date |
Nov 04, 2019 |
| Last update date |
Nov 10, 2020 |
| Contact name |
Enrique Blanco |
| E-mail(s) |
enrique.blanco@crg.eu
|
| Phone |
+34 93 316 01 00
|
| Organization name |
Center for Genomic Regulation (CRG)
|
| Department |
Gene Regulation, Stem Cells and Cancer
|
| Lab |
Epigenetic Events in Cancer (L. Di Croce's lab)
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE139884 |
Huntington’s disease as a lamin B1 nuclear envelopathy |
|
| Relations |
| BioSample |
SAMN13191143 |
| SRA |
SRX7098815 |
