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| Status |
Public on Sep 10, 2019 |
| Title |
HiC_IMR90_MYOD_GM_Rep1 |
| Sample type |
SRA |
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| Source name |
IMR90
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Lung fibroblast-derived myoblast
ectopic gene expression: mouse MYOD overexpression
passage from isolation: passage 21-28
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| Treatment protocol |
IMR90 cells were transfected with vector containing TET-inducible MYOD or EMPTY vector control, cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and collected for GM time point. Cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and for 3days in EMEM 2% HS 1%ITS collected for DM time point. Cells were then treated or not with hTNF for 1hr prior collection
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| Growth protocol |
IMR90 cells were cultured in EMEM supplemented with 10% FBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For RNASeq: cells were lyzed with Trizol and RNA was extracted following manufacturer's instruction. For Hi-C, DNA crossliked, digested and ligated, ligation products were isolated with streptavidine beads, Hi-C experiment were conducted in biological replicates using DpnIII, according to the protocol published by Rao et al, 2014 with slight modifications
RNASeq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit set A RS-122-2101 following Illumina's recomandations. Hi-C experiment were conducted in biological replicates using DpnIII, according to the protocol published by Rao et al, 2014 with slight modifications
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
processed data file: GSE98509_E_GMvsM_GM_differentials.txt
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| Data processing |
ChIP-Seq - Read quality was determined using FASTQC. Reads were mapped using bowtie2-2.0.5/bowtie2 to the female Homo sapiens hg19 genomes with options: --very-sensitive-local. Peaks were called using macs2 2.1.1.20160309 with qvalue=0.01, macs2 2.1.1.20160309 was also used for differential peak calling among samples.
RNA-Seq - Spike-in were added based on number of nuclei but were not used for the analysis. Read quality was determined using FASTQC. Reads were mapped using TopHat2.1.1 to the female Homo sapiens hg19 genomes with options: -p 8 -g 1 --segment-length 17 --library-type fr-firststrand. HTSeq-0.6.1p1173 with --stranded=reverse option was used to assigned mapped reads to Homo Sapiens GRCh37.75 genes. Differential expression analysis was performed using DESeq2.
Hi-C - Read quality was determined using FASTQC. HiCPro-v2.7.7 was used for read mapping, valid ligation product detection, quality control, and sparse chromosomal interaction maps. HiTC was used to transform sparse matrices to NbyN matrices. Differential interactions 4kb resolution were called by DiffHiC. Requirement for significant differential interaction: Log(Fold Change) lower than -2 or higher than 2, pvalue lower than 0.05. Boundaries were called following a previously described method (Crane et al., 2015)
Genome_build: hg19
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| Submission date |
May 03, 2017 |
| Last update date |
Sep 10, 2019 |
| Contact name |
Alessandra Dall'Agnese |
| E-mail(s) |
aled@wi.mit.edu
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| Organization name |
Whitehead Institute
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| Street address |
455 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE98509 |
MYOD Remodeling of the Genome Architecture during Myogenic Conversion of Somatic Cells |
| GSE98530 |
Re-Wiring 3D Nuclear Architecture by a Single Transcription Factor during Somatic Cell Reprogramming |
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| Relations |
| BioSample |
SAMN06887608 |
| SRA |
SRX2781964 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2597684_M_GM_exp09_40000_iced.matrix.txt.gz |
784.8 Mb |
(ftp)(http) |
TXT |
| GSM2597684_M_GM_exp09_4000_iced.matrix.txt.gz |
1.7 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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