|
| Status |
Public on Jan 01, 2023 |
| Title |
D0_LMNA_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Adipose
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human primary adipose stem cells
tissue: Adipose
time: Day 0
chip antibody: LMNA/C (Santa Cruz sc-7292)
replicate: Rep2
|
| Treatment protocol |
Proliferating cells were harvested, re-seeded at confluency and cultured confluent for 48 h without fibroblast growth factor. On Day 0, ASCs were induced to differentiate with 10 µg/ml insulin, 200 µM indomethacin, 1 µM dexamethasone and 0.5 µM 3-isobutyl-1-methylxanthine. Cells were collected at indicated timepoints for protein, RNA and chromatin preparations and analyses.
|
| Growth protocol |
Human normal ASCs purifed from adipose tissue were cultured in proliferating state in DMEM/F12 containing 10 % fetal calf serum and 20 ng/ml basic fibroblast growth factor.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP, cells were sonicated to produce chromatin fragments of 200 base-pairs, lysates were clarified by sedimentation and histone-DNA or lamin-DNA complexes were isolated from supernatants by ChIP using specific antibodies. RNA was purified from cell lysates using the RNEasy mini kit (Qiagen).
ChIP sequencing libraries were prepared according to Illumina protocols for sequencing at the Norwegian Sequencing Center.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ASCs on the day of adipogenic induction
|
| Data processing |
ChIP-seq reads were aligned to the hg38 reference genome using bowtie2 version 2.4.1
For histone ChIPs with replicates, bams files were merged. For LMNA ChIPs, replicates were merged after peak calling.
Duplicate reads were removed using picard MarkDuplicates. For histone ChIPs multi-mapping reads and alignments with a mapping quality below 10 were also filtered out.
For histone modification ChIPseq, peaks were called using macs2 2.2.7.1. For H3K27me3, H3K36me3 and H3K4me1 option --broad was used.
For LMNA ChIPseq, peak calling was done using Enriched Domain Detector (EDD) version 1.1.15, run 10 times on each sample to optimize BinSize and GapPenalty settings before a final run with optimized settings.
Assembly: hg38
Supplementary files format and content: Bed EDD peak file - 4th column is EDD score.
Supplementary files format and content: bigwig (.bw) files are regular bigwig files are log2ratio of filtered ChIP/Input files, generated using bamCompare from deeptools 3.5.1 if the extension is ".grep.norm.bw". Else if the tracks ends "_pileup.norm.bw" the track is generated from macs output files as the log 10 ratio of treat/control lamba pileup files.
Supplementary files format and content: .narrowPeak and .broadPeak files are modified bed files created by macs2 callpeaks
|
| |
|
| Submission date |
Dec 19, 2022 |
| Last update date |
Jan 02, 2023 |
| Contact name |
Philippe Collas |
| Organization name |
University of Oslo
|
| Department |
Institute of Basic Medical Sciences
|
| Street address |
PO Box 1112 Blindern
|
| City |
Oslo |
| ZIP/Postal code |
0317 |
| Country |
Norway |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE221288 |
Gene regulatory loops at lamina-associated domains |
|
| Relations |
| BioSample |
SAMN32308529 |
| SRA |
SRX18768994 |
