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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 01, 2019 |
| Title |
ATAC-seq_Pgk_d1_rep2 |
| Sample type |
SRA |
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| Source name |
mouse ESC (Pgk12.1)
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| Organism |
Mus musculus |
| Characteristics |
cell type: mouse ESC (Pgk12.1)
strain: XX, 129/Ola-Hsd x (C3H/He-Pgk-1a/Ws x 129/Ola-Hsd)F1
genotype: wild type
differentiation stage: day 1
capture-c viewpoint: NA
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| Growth protocol |
Feeder-independent male mouse ESC (E14) were grown on gelatin-coated flasks in Glasgow medium supplemented with 2 mM L-Glutamine, 0.1 mM NEAA and 1 mM sodium pyruvate (GIBCO) with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma), 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Feeder-independent female mouse ESC (Pgk12.1) were grown on gelatin-coated flasks in DMEM supplemented with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma) and 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Cells were cultivated in 8% CO2, and passaged when needed. Medium was changed daily. Cells were checked for mycoplasma infection every 3-4 months and tested negative.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For Chromosome Conformation Capture (5C and Capture-C) cells were fixed in culture plates or flasks and scraped off. For RNA-seq cells were washed once with PBS and lysed in Trizol in the culture plate. For ATAC-seq, cells were washed once with PBS and directly incubated in the transposition reaction.
5C libraries were generated based on a custom Illumina-compatible protocol (Nora et al 2017); Capture-C libraries were generated using KAPA Hyper Prep Kit (KK8500, Kapa Biosystems); RNA-seq libraries were generated using the TruSeq Stranded Total RNA kit (Illumina); ATAC-seq libraries were generated based on a Nextseq-compatible protocol (Buenrostro et al 2013).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
rafael_XXd1_idrValues_withpool_thrp05.bed
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| Data processing |
5C sequencing reads were processed using 5C-Pro pipeline, available at https://github.com/bioinfo-pf-curie/5C-Pro. Single-end sequencing reads are trimmed and aligned using bowtie2. Quality controls were performed using the HiTC BioConductor package.
Capture-C sequencing reads were trimmed using the Trim Galore! pipeline (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and then processed using the HiC-Pro pipeline 72 (v2.8.0).
RNA sequencing reads were aligned on the mouse genome using the STAR mapper. Raw counts have been generated from the STAR mapper using the GENCODE annotation database vM1.
ATAC-seq paired-end reads were trimmed of the adaptor sequences and aligned to the NCBIm37 genome using STAR v2.4.2a. Duplicate fragments were removed using PICARD tools v1.90, only unique mapped fragments between 38bp and 1500bp in length were retained. ATAC-seq peaks were called on the 1bp transposase cut-sites using MACS2 (with shift size 100 and extension size 200). Only the peaks considered reproducible by IDR (version 2), with an IDR threshold of 0.05, were kept.
Genome_build: mm9 / NCBIm37
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| Submission date |
Jan 03, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Nicolas Servant |
| E-mail(s) |
Nicolas.Servant@curie.fr
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| Organization name |
Institut Curie
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| Street address |
26 rue d'ulm
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| City |
Paris Cedex 05 |
| ZIP/Postal code |
75248 |
| Country |
France |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE124596 |
A conserved noncoding locus modulates random monoallelic Xist expression across a TAD boundary |
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| Relations |
| BioSample |
SAMN10688897 |
| SRA |
SRX5197725 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3537422_rafael_XXd1rep2_mm9_Aligned.1bp.bin20s60.blacklist.norm.bw |
475.7 Mb |
(ftp)(http) |
BW |
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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