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https://github.com/mahshaaban/adiporeg_chip
Collect, process and quality control Chromatin Immunoprecipitation followed by sequencing (ChIP-Seq) data from differentiating 3T3-L1.
https://github.com/mahshaaban/adiporeg_chip
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Collect, process and quality control Chromatin Immunoprecipitation followed by sequencing (ChIP-Seq) data from differentiating 3T3-L1.
- Host: GitHub
- URL: https://github.com/mahshaaban/adiporeg_chip
- Owner: MahShaaban
- Created: 2018-10-13T10:46:18.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2018-11-02T06:05:21.000Z (about 6 years ago)
- Last Synced: 2023-08-03T15:25:10.420Z (over 1 year ago)
- Language: TeX
- Homepage:
- Size: 43.9 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# adiporeg_chip
Collect, process and quality control Chromatin Immunoprecipitation followed by sequencing (ChIP-Seq) data from differentiating 3T3-L1. Related repositories to collect and process other kinds of data are [adiporeg_rna](https://github.com/MahShaaban/adiporeg_rna) and [adiporeg_dhs](https://github.com/MahShaaban/adiporeg_dhs). The processed data are further analyzed in repositories such as [adiporeg](https://github.com/MahShaaban/adiporeg)
This repository aims to detail the following:
1. The search strategy
2. The collected data
3. The pre-processing and the processing of the raw data
## 1. The search strategy
The term "3T3-L1" was used to search the NCBI **SRA** repository. The results were sent to the **run selector**. 1,176 runs were viewed. The runs were faceted by **Assay Type** and the "chip-seq" which resulted in 739 runs. Only 235 samples from 20 different studies were included after being manually reviewed to fit the following criteria:
* The raw data is available from GEO and has a GEO identifier (GSM#)
* The raw data is linked to a published publicly available article
* The protocols for generating the data sufficiently describe the origin of the cell line, the differentiation medium and the time points when the samples were collected.
* In case the experimenal designs included treatment other than the differentiation medias, the control (non-treated) samples were included.
Note: The data quality and the platform discrepencies are not inluded in these criteria
## 2. The collected data
### 2.1 Sample table
| Stage | Time (hours) | Samples | Factors |
|-------|--------------|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Early | -48 | 7 | CTCF/H3K27ac/H3K27me3/H3K36me3/H3K4me1/H3K4me2/H3K4me3 |
| | 0 | 56 | POLR2A/PPARG/RXRG/CTCF/H3K27ac/H3K27me3/H3K36me3/H3K4me1/H3K4me2/H3K4me3/None/CEBPB/H3K9ac/CEBPD/KDM1A/NRF1/GPS2/H3K9me3/SETDB1/MBD1/KDM5A/SMC1A/EP300/NCOR1/MED1/HDAC3/HDAC2 |
| | 2 | 1 | CEBPB |
| | 4 | 43 | POLR2A/RXRG/STAT5A/NR3C1/CEBPD/CEBPB/ATF2/ATF7/JUN/FOSL2/KLF4/KLF5/PBX1/STAT1/VDR/RXR/MED1/EP300/BRG1/H3K27ac/H3K4me1/H3K4me2/KDM5A/H3K4me3/SMC1A/NCOR1/HDAC3/HDAC2/CTCF |
| | 6 | 3 | None/NR3C1/CEBPB |
| | 24 | 6 | POLR2A/PPARG/RXRG/None/H3K9ac/TCF7 |
| | 48 | 24 | POLR2A/PPARG/RXRG/CTCF/H3K27ac/H3K27me3/H3K36me3/H3K4me1/H3K4me2/H3K4me3/CEBPB/KDM5A/KDM5C/SMC1A/MED1 |
| | 72 | 3 | POLR2A/PPARG/RXRG |
| | NA | 25 | PSMB1/CREB1/JUN/PPARG/None/Ubiquitin/H3K9me2/H3K27me3/H3K4me3/H3K27ac/H3K36me3/H3K4me1/H3K79me2/H3K79me3/H4K20me1/CEBPB |
| Late | 96 | 9 | POLR2A/PPARG/RXRG/SMC1A/MED1/CTCF |
| | 144 | 7 | POLR2A/PPARG/RXRG/H3K9me3/SETDB1 |
| | 168 | 29 | CTCF/H3K27ac/H3K27me3/H3K36me3/H3K4me1/H3K4me2/H3K4me3/PPARG/None/H3K9me3/MED1/CEBPA/POLR2A/CREB1/KDM1A/KMT2B/SMC1A |
| | 192 | 1 | H3K4me3 |
| | 240 | 2 | None/H3K9ac |
| | NA | 20 | E2F4/CEBPA/EP300/None/H3K9ac/PPARG/MED1/CREB1/NCOR1/CEBPB/ATF2/JUND/FOSL2 |
### 2.2 Run table
| Study | Samples | Runs |
|-----------|------------|------|
| GSE13511 | GSM340794 | 3 |
| | GSM340795 | 3 |
| | GSM340796 | 4 |
| | GSM340797 | 3 |
| | GSM340798 | 3 |
| | GSM340799 | 3 |
| | GSM340800 | 2 |
| | GSM340801 | 2 |
| | GSM340802 | 3 |
| | GSM340803 | 2 |
| | GSM340804 | 3 |
| | GSM340805 | 2 |
| | GSM340806 | 2 |
| | GSM340807 | 2 |
| | GSM340808 | 2 |
| | GSM340809 | 2 |
| | GSM340810 | 2 |
| | GSM340811 | 2 |
| GSE17067 | GSM427092 | 1 |
| | GSM427094 | 1 |
| | GSM427095 | 1 |
| | GSM427097 | 1 |
| GSE21314 | GSM532740 | 1 |
| | GSM532744 | 1 |
| GSE21365 | GSM535740 | 9 |
| | GSM535741 | 3 |
| | GSM535742 | 2 |
| | GSM535743 | 2 |
| | GSM535744 | 2 |
| | GSM535745 | 4 |
| | GSM535746 | 2 |
| | GSM535747 | 2 |
| | GSM535748 | 4 |
| | GSM535749 | 2 |
| | GSM535750 | 2 |
| | GSM535751 | 2 |
| | GSM535752 | 2 |
| | GSM535753 | 4 |
| | GSM535754 | 2 |
| | GSM535755 | 3 |
| | GSM535756 | 3 |
| | GSM535757 | 3 |
| | GSM535758 | 2 |
| | GSM535759 | 4 |
| | GSM535760 | 2 |
| | GSM535761 | 2 |
| | GSM535762 | 4 |
| | GSM535763 | 3 |
| | GSM535764 | 3 |
| | GSM535765 | 3 |
| | GSM535766 | 2 |
| | GSM535767 | 4 |
| | GSM535768 | 2 |
| | GSM535769 | 2 |
| | GSM535770 | 2 |
| GSE21898 | GSM544717 | 1 |
| | GSM544718 | 1 |
| | GSM544719 | 1 |
| | GSM544720 | 1 |
| | GSM544721 | 1 |
| | GSM544722 | 1 |
| | GSM544723 | 1 |
| | GSM544724 | 1 |
| | GSM544725 | 1 |
| | GSM544726 | 1 |
| GSE27826 | GSM686970 | 1 |
| | GSM686971 | 1 |
| | GSM686972 | 1 |
| | GSM686973 | 1 |
| | GSM686974 | 1 |
| | GSM686975 | 1 |
| | GSM686976 | 1 |
| | GSM686977 | 1 |
| | GSM686978 | 1 |
| | GSM686979 | 1 |
| | GSM686980 | 1 |
| | GSM686981 | 1 |
| | GSM686982 | 1 |
| | GSM686983 | 1 |
| GSE31867 | GSM790410 | 1 |
| GSE33821 | GSM1095377 | 1 |
| | GSM1095378 | 1 |
| | GSM1095379 | 1 |
| | GSM1095381 | 1 |
| | GSM838021 | 1 |
| | GSM838022 | 1 |
| GSE41455 | GSM1017630 | 18 |
| | GSM1017631 | 14 |
| | GSM1017632 | 48 |
| | GSM1017633 | 56 |
| | GSM1017634 | 16 |
| | GSM1017635 | 44 |
| | GSM1017636 | 48 |
| GSE49423 | GSM1199128 | 4 |
| | GSM1199130 | 2 |
| | GSM1199132 | 1 |
| | GSM1199134 | 2 |
| | GSM1199136 | 1 |
| | GSM1199138 | 1 |
| | GSM1199140 | 1 |
| | GSM1199142 | 1 |
| GSE50934 | GSM1232698 | 1 |
| | GSM1232699 | 1 |
| | GSM1232700 | 1 |
| | GSM1232701 | 1 |
| | GSM1232706 | 1 |
| | GSM1232707 | 1 |
| GSE56745 | GSM1368000 | 1 |
| | GSM1368002 | 2 |
| | GSM1368003 | 2 |
| | GSM1368005 | 1 |
| | GSM1368007 | 1 |
| | GSM1368009 | 1 |
| | GSM1368011 | 1 |
| | GSM1368012 | 1 |
| | GSM1368013 | 1 |
| | GSM1368014 | 1 |
| | GSM1368015 | 1 |
| GSE56872 | GSM1370447 | 1 |
| | GSM1370448 | 1 |
| | GSM1370449 | 1 |
| | GSM1370450 | 1 |
| | GSM1370452 | 1 |
| | GSM1370453 | 1 |
| | GSM1370454 | 1 |
| | GSM1370455 | 1 |
| | GSM1370456 | 1 |
| | GSM1370457 | 1 |
| | GSM1370466 | 1 |
| | GSM1370467 | 1 |
| | GSM1370468 | 1 |
| | GSM1370469 | 1 |
| | GSM1370470 | 1 |
| | GSM1370471 | 1 |
| | GSM1370472 | 1 |
| | GSM1370473 | 1 |
| | GSM1370474 | 1 |
| GSE57777 | GSM1388416 | 1 |
| | GSM1388417 | 1 |
| GSE58491 | GSM1412512 | 1 |
| | GSM1412513 | 1 |
| | GSM1412514 | 1 |
| | GSM1412515 | 1 |
| | GSM1412516 | 1 |
| | GSM1412517 | 1 |
| | GSM1412518 | 1 |
| | GSM1412519 | 1 |
| | GSM1412520 | 1 |
| GSE73432 | GSM1893623 | 1 |
| | GSM1893624 | 1 |
| | GSM1893625 | 2 |
| | GSM1893626 | 1 |
| | GSM1893628 | 2 |
| | GSM1893629 | 1 |
| | GSM1893630 | 2 |
| | GSM1893631 | 1 |
| | GSM1893632 | 1 |
| | GSM1893633 | 1 |
| | GSM1893634 | 2 |
| | GSM1893636 | 2 |
| | GSM1893637 | 1 |
| | GSM1893649 | 1 |
| GSE74189 | GSM2522176 | 1 |
| | GSM2522177 | 1 |
| GSE84410 | GSM2233356 | 1 |
| | GSM2233357 | 1 |
| | GSM2233358 | 1 |
| | GSM2233359 | 1 |
| | GSM2233360 | 1 |
| | GSM2233361 | 1 |
| | GSM2233368 | 1 |
| | GSM2233369 | 1 |
| | GSM2233370 | 1 |
| | GSM2233371 | 1 |
| | GSM2233373 | 1 |
| | GSM2391498 | 1 |
| | GSM2391499 | 1 |
| | GSM2391500 | 1 |
| | GSM2391501 | 1 |
| GSE85100 | GSM2257695 | 2 |
| | GSM2257696 | 2 |
| | GSM2257705 | 2 |
| | GSM2257706 | 2 |
| GSE95533 | GSM2515924 | 1 |
| | GSM2515925 | 1 |
| | GSM2515926 | 1 |
| | GSM2515927 | 1 |
| | GSM2515928 | 1 |
| | GSM2515929 | 1 |
| | GSM2515930 | 1 |
| | GSM2515931 | 1 |
| | GSM2515932 | 1 |
| | GSM2515933 | 1 |
| | GSM2515936 | 1 |
| | GSM2515937 | 1 |
| | GSM2515940 | 1 |
| | GSM2515941 | 1 |
| | GSM2515944 | 1 |
| | GSM2515945 | 1 |
| | GSM2515946 | 1 |
| | GSM2515947 | 1 |
| | GSM2515948 | 1 |
| | GSM2515949 | 1 |
| | GSM2515950 | 1 |
| | GSM2515951 | 1 |
| | GSM2515952 | 1 |
| | GSM2515953 | 1 |
| | GSM2515954 | 1 |
| | GSM2515955 | 1 |
| | GSM2515956 | 1 |
| | GSM2515957 | 1 |
| | GSM2515958 | 1 |
| | GSM2515959 | 1 |
| | GSM2515960 | 1 |
| | GSM2515961 | 1 |
| | GSM2515962 | 1 |
| | GSM2515963 | 1 |
| | GSM2515964 | 1 |
| | GSM2515965 | 1 |
| | GSM2515966 | 1 |
| | GSM2515967 | 1 |
| | GSM2515968 | 1 |
| | GSM2515969 | 1 |
| | GSM2515970 | 1 |
| | GSM2515971 | 1 |
| | GSM2515972 | 1 |
| | GSM2515973 | 1 |
| | GSM2515974 | 1 |
| | GSM2515975 | 1 |
| | GSM2515976 | 1 |
| | GSM2515977 | 1 |
| | GSM2515978 | 1 |
| | GSM2515979 | 1 |
| | GSM2515980 | 1 |
| | GSM2515981 | 1 |
| Library Type | Runs |
|--------------|------|
| PAIRED | 8 |
| SINGLE | 564 |
| Sequencer Models | Runs |
|------------------------------|------|
| Illumina Genome Analyzer | 148 |
| Illumina Genome Analyzer II | 18 |
| Illumina Genome Analyzer IIx | 45 |
| Illumina HiSeq 1500 | 73 |
| Illumina HiSeq 2000 | 278 |
| Illumina HiSeq 2500 | 2 |
| NextSeq 500 | 8 |
### 2.3 Studies
[1] A. S. B. Brier, A. Loft, J. G. Madsen, et al. “The KDM5 family is required
for activation of pro-proliferative cell cycle genes during adipocyte
differentiation”. In: _Nucleic Acids Research_ 45.4 (2017), pp. 1743-1759. ISSN:
13624962. DOI: 10.1093/nar/gkw1156. eprint: 1611.06654.
[2] M. D. Cardamone, B. Tanasa, M. Chan, et al. “GPS2/KDM4A pioneering activity
regulates promoter-specific recruitment of PPARG”. In: _Cell Reports_ 8.1 (2014),
pp. 163-176. ISSN: 22111247. DOI: 10.1016/j.celrep.2014.05.041. eprint:
NIHMS150003.
[3] A. Catic, C. Y. Suh, C. T. Hill, et al. “Genome-wide Map of nuclear protein
degradation shows NCoR1 turnover as a key to mitochondrial gene regulation”. In:
_Cell_ 155.6 (2013), pp. 1380-1395. ISSN: 00928674. DOI:
10.1016/j.cell.2013.11.016. eprint: NIHMS150003.
[4] A. G. Cristancho, M. Schupp, M. I. Lefterova, et al. “Repressor transcription
factor 7-like 1 promotes adipogenic competency in precursor cells”. In:
_Proceedings of the National Academy of Sciences_ 108.39 (2011), pp. 16271-16276.
ISSN: 0027-8424. DOI: 10.1073/pnas.1109409108. .
[5] D. Duteil, E. Metzger, D. Willmann, et al. “LSD1 promotes oxidative
metabolism of white adipose tissue”. In: _Nature Communications_ 5.May (Jun.
2014), p. 4093. ISSN: 20411723. DOI: 10.1038/ncomms5093. .
[6] A. K. Haakonsson, M. Stahl Madsen, R. Nielsen, et al. “Acute Genome-Wide
Effects of Rosiglitazone on PPARG Transcriptional Networks in Adipocytes”. In:
_Molecular Endocrinology_ 27.9 (2013), pp. 1536-1549. ISSN: 0888-8809. DOI:
10.1210/me.2013-1080. .
[7] S. Kang, L. T. Tsai, Y. Zhou, et al. “Identification of nuclear hormone
receptor pathways causing insulin resistance by transcriptional and epigenomic
analysis”. In: _Nature Cell Biology_ 17.1 (2015), pp. 44-56. ISSN: 14764679. DOI:
10.1038/ncb3080. eprint: NIHMS150003.
[8] B. Lai, J. E. Lee, Y. Jang, et al. “MLL3/MLL4 are required for CBP/p300
binding on enhancers and super-enhancer formation in brown adipogenesis”. In:
_Nucleic Acids Research_ 45.11 (2017), pp. 6388-6403. ISSN: 13624962. DOI:
10.1093/nar/gkx234.
[9] M. I. Lefterova, D. J. Steger, D. Zhuo, et al. “Cell-Specific Determinants of
Peroxisome Proliferator-Activated Receptor Function in Adipocytes and
Macrophages”. In: _Molecular and Cellular Biology_ 30.9 (2010), pp. 2078-2089.
ISSN: 0270-7306. DOI: 10.1128/MCB.01651-09. .
[10] X. Luo, K. W. Ryu, D. S. Kim, et al. “PARP-1 Controls the Adipogenic
Transcriptional Program by PARylating C/EBPB and Modulating Its Transcriptional
Activity”. In: _Molecular Cell_ 65.2 (Jan. 2017), pp. 260-271. ISSN: 10974164.
DOI: 10.1016/j.molcel.2016.11.015. .
[11] K. D. Macisaac, K. A. Lo, W. Gordon, et al. “A quantitative model of
transcriptional regulation reveals the influence of binding location on
expression”. In: _PLoS Computational Biology_ 6.4 (Apr. 2010), p. e1000773. ISSN:
1553734X. DOI: 10.1371/journal.pcbi.1000773. .
[12] Y. Matsumura, R. Nakaki, T. Inagaki, et al. “H3K4/H3K9me3 Bivalent Chromatin
Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte
Differentiation”. In: _Molecular Cell_ 60.4 (2015), pp. 584-596. ISSN: 10974164.
DOI: 10.1016/j.molcel.2015.10.025.
[13] T. S. Mikkelsen, Z. Xu, X. Zhang, et al. “Comparative epigenomic analysis of
murine and human adipogenesis”. In: _Cell_ 143.1 (Oct. 2010), pp. 156-169. ISSN:
00928674. DOI: 10.1016/j.cell.2010.09.006. .
[14] R. Nielsen, T. \. Pedersen, D. Hagenbeek, et al. “Genome-wide profiling of
PPARG:RXR and RNA polymerase II occupancy reveals temporal activation of distinct
metabolic pathways and changes in RXR dimer composition during adipogenesis”. In:
_Genes and Development_ 22.21 (2008), pp. 2953-2967. ISSN: 08909369. DOI:
10.1101/gad.501108.
[15] R. Siersbæk, J. G. S. Madsen, B. M. Javierre, et al. “Dynamic Rewiring of
Promoter-Anchored Chromatin Loops during Adipocyte Differentiation”. In:
_Molecular Cell_ 66.3 (2017), pp. 420-435.e5. ISSN: 10974164. DOI:
10.1016/j.molcel.2017.04.010.
[16] R. Siersbaek, R. Nielsen, S. John, et al. “Extensive chromatin remodelling
and establishment of transcription factor hotspots during early adipogenesis”.
In: _EMBO Journal_ 30.8 (Apr. 2011), pp. 1459-1472. ISSN: 02614189. DOI:
10.1038/emboj.2011.65. .
[17] R. Siersbæk, A. Rabiee, R. Nielsen, et al. “Transcription factor
cooperativity in early adipogenic hotspots and super-enhancers”. In: _Cell
Reports_ 7.5 (Jun. 2014), pp. 1443-1455. ISSN: 22111247. DOI:
10.1016/j.celrep.2014.04.042. .
[18] D. J. Steger, G. R. Grant, M. Schupp, et al. “Propagation of adipogenic
signals through an epigenomic transition state”. In: _Genes and Development_
24.10 (May. 2010), pp. 1035-1044. ISSN: 08909369. DOI: 10.1101/gad.1907110. .
[19] S. E. Step, H. W. Lim, J. M. Marinis, et al. “Anti-diabetic rosiglitazone
remodels the adipocyte transcriptome by redistributing transcription to
PPARG-driven enhancers”. In: _Genes and Development_ 28.9 (May. 2014), pp.
1018-1028. ISSN: 15495477. DOI: 10.1101/gad.237628.114. .
[20] L. Wang, S. Xu, J. E. Lee, et al. “Histone H3K9 methyltransferase G9a
represses PPARG expression and adipogenesis”. In: _EMBO Journal_ 32.1 (2013), pp.
45-59. ISSN: 02614189. DOI: 10.1038/emboj.2012.306.
## 3. The pre-processing and the processing of the raw data
The scripts to download and process the raw data are located in `scripts/` and are glued together to run sequentially by the GNU make file `Makefile`. The following is basically a description of the recipies in the `Makefile` with emphasis on the software versions, options, inputs and outputs.
### 3.1 `download_fastq`
* Program: `wget` (1.18)
* Input: `run.csv`, the URLs column
* Output: `*.fastq.gz`
* Options: `-N`
### 3.2 `get_annotation`
* Program: `wget` (1.18)
* Input: URL for mm10 gene annotation file
* Output: `annotation.gtf`
* Options: `-N`
### 3.3 `make_index`
* Program: `bowtie2-build` (2.3.0)
* Input: URL for mm10 mouse genome fasta files
* Output: `*.bt2` bowtie2 index for the mouse genome
* Options: defaults
### 3.4 `align_reads`
* Program: `bowtie2` (2.3.0)
* Input: `*.fastq.gz` and `mm10/` bowtie2 index for the mouse genome
* Output: `*.sam`
* Options: `--no-unal`
### 3.5 `sam_to_bam`
* Program: `samtools view` (1.3.1)
* Input: `*.sam`
* Output: `*.bam`
* Options: `-Sb`
### 3.6 `bam_sort_index`
* Program: `samtools sort` and `samtools index` (1.3.1)
* Input: `*.bam`
* Output: `*.bam` and `*.bai`
* Option: defaults
### 3.7 `count_features`
* Program: `featureCounts` (1.5.1)
* Input: `*.bam` and the annotation `gtf` file for the mm10 mouse genome.
* Output: `*.txt`
* Option: defaults
### 3.8 `fastqc`
* Program: `fastqc` (0.11.5)
* Input: `*.fastq.gz`, `*.sam` and `*.bam`
* Output: `*_fastqc.zip`
* Option: defaults