|
| Status |
Public on Jun 27, 2019 |
| Title |
MeCP2 KO ATAC-seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
LUHMES-derived neurons
|
| Organism |
Homo sapiens |
| Characteristics |
div: Day 9
passage: 15-20
cell line: LUHMES
cell type: LUHMES-derived neurons
genotype: MeCP2 KO
|
| Treatment protocol |
Cells were modified using CRISPR system for KO and infected with lentiviruses carrying MeCP2 for OE.
|
| Growth protocol |
LUHMES cells were cultured and differentiated according to published protocol (Shah et al., 2016).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Neurons were scraped from the plate and nuclei were isolated using hypotonic buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3mM MgCl2, 0.1% [v/v] Igepal CA-630) and counted. 50,000 nuclei were resuspended in 50 µl transposition reaction mix containing 2.5 µl Nextera Tn5 Transposase and 2x TD Nextera reaction buffer. The reaction was incubated for 30 min at 37 ºC.
DNA was purified by either MinElute PCR kit (Qiagen) or Agencourt AMPure XP (Beckman Coulter) beads and PCR amplified with NEBNext High Fidelity reaction mix (NEB) to generate a sequencing library.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Tn5 transposed chromatin
h_MeCP2_KO_D10_113
|
| Data processing |
Pre-process reads with Trimmomatic version 0.32 ILLUMINACLIP:nextera.fa:2:40:15 MINLEN:25
Align to genome with bwa v0.7.5a-r405
Filter for unique primary alignments with Samtools 1.3.1
Remove duplicate reads with Picard v1.107
Remove mitochondrial reads and blacklisted regions with bedtools 2.27
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files of aligned reads
|
| |
|
| Submission date |
Jan 25, 2019 |
| Last update date |
Jun 27, 2019 |
| Contact name |
Shaun Michael Webb |
| E-mail(s) |
shaun.webb@ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
Wellcome Trust Centre for Cell Biology
|
| Lab |
Bioinformatics Core Facility
|
| Street address |
2.21 Swann Building, Kings Buildings
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE125658 |
Study of MeCP2 binding and accessibity of chromatin in absence and presence of MeCP2 using ATAC-seq |
| GSE125660 |
Study of MeCP2 in LUHMES-derived neurons |
|
| Relations |
| BioSample |
SAMN10819782 |
| SRA |
SRX5291865 |
