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Sample GSM5605570 Query DataSets for GSM5605570
Status Public on Mar 21, 2022
Title RNAseq_T04_Rep2
Sample type SRA
Source name Human primary adipose stem cells
Organism Homo sapiens
Characteristics time point: 04 Hours (T04)
cell type: ASCs on 04 hours after adipogenic induction
replicate: Rep2
Treatment protocol Proliferating cells were harvested, re-seeded at confluency and cultured confluent for 48 h without fibroblast growth factor. At T00, ASCs were induced to differentiate with 10 µg/ml insulin, 200 µM indomethacin, 1µM 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 total RNA
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-seq and RNA-seq sequencing libraries were prepared according to Illumina protocols for sequencing on a Nextseq500 or Novaseq (ChIP-seq) or on a Nextseq500 (RNA-seq) at the Norwegian Sequencing Center.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing ChIP-seq and RNAseq reads were aligned to the hg38 reference genome using bowtie2 version 2.4.1 for ChIP-seq reads and BWA-MEM version 0.7.12 for RNAseq reads
Duplicate reads were removed using picard MarkDuplicates
For RNA-seq, reads per transcript were counted using featureCounts from Subread package 2.0.1. Differential gene expression was determined using DESeq2 1.30.0.
For histone modification ChIPseq, H3K4me1 peaks were called from both replicated using macs2 .
For LMNB1 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.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files with 4 columns: chromosome, start position, end position, score
Supplementary_files_format_and_content: featureCounts.txt : tab-delimited text files with 2 columns: transcript ID , read count
Supplementary_files_format_and_content: DESeq2_counts.txt : tab-delimited text files with 2 columns: transcript ID , DESeq2 normalized count
Supplementary_files_format_and_content: bed files with 4 columns: chromosome, start position, end position, score
Supplementary_files_format_and_content: Bigwig file with log2ratio ChIP/Input were generated using bamCompare from deeptools 3.5.1.
Submission date Sep 30, 2021
Last update date Mar 21, 2022
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 GPL18573
Series (1)
GSE185066 Local euchromatin enrichment in lamina-associated domains anticipates their re-positioning in the adipogenic lineage
BioSample SAMN21909283
SRA SRX12412380

Supplementary file Size Download File type/resource
GSM5605570_T04_Rep2_DESeq2_counts.txt.gz 277.1 Kb (ftp)(http) TXT
GSM5605570_T04_Rep2_featureCounts.txt.gz 250.7 Kb (ftp)(http) TXT
GSM5605570_T04_Rep2_hg38_MappedData_bedgraph.bedgraph.gz 15.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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