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Sample GSM6857887 Query DataSets for GSM6857887
Status Public on Jan 01, 2023
Title D3_LMNA_Rep1
Sample type SRA
 
Source name Adipose
Organism Homo sapiens
Characteristics cell type: Human primary adipose stem cells
tissue: Adipose
time: Day 3
chip antibody: LMNA/C (Santa Cruz sc-7292)
replicate: Rep1
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 day 3 after 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 SAMN32308526
SRA SRX18768997

Supplementary file Size Download File type/resource
GSM6857887_ASC_D3_LMNAC_Rep1_log_ratio_1KB.bedgraph.gz 21.1 Mb (ftp)(http) BEDGRAPH
GSM6857887_ASC_D3_LMNAC_Rep1_peaks.bed.gz 5.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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