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| Status |
Public on Mar 21, 2022 |
| Title |
RNAseq_T00_Rep2 |
| Sample type |
SRA |
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| Source name |
Human primary adipose stem cells
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| Organism |
Homo sapiens |
| Characteristics |
time point: 00 Hours (T00)
cell type: ASCs on the day of differentiation induction
replicate: Rep2
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| 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.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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 2.2.7.1 .
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.
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| Submission date |
Sep 30, 2021 |
| Last update date |
Mar 21, 2022 |
| Contact name |
Philippe Collas |
| Organization name |
University of Oslo
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| Department |
Institute of Basic Medical Sciences
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| Street address |
PO Box 1112 Blindern
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| City |
Oslo |
| ZIP/Postal code |
0317 |
| Country |
Norway |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE185066 |
Local euchromatin enrichment in lamina-associated domains anticipates their re-positioning in the adipogenic lineage |
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| Relations |
| BioSample |
SAMN21909206 |
| SRA |
SRX12412378 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5605568_T00_Rep2_DESeq2_counts.txt.gz |
288.9 Kb |
(ftp)(http) |
TXT |
| GSM5605568_T00_Rep2_featureCounts.txt.gz |
253.9 Kb |
(ftp)(http) |
TXT |
| GSM5605568_T00_Rep2_hg38_MappedData_bedgraph.bedgraph.gz |
17.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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