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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 10, 2022 |
| Title |
19-T4_S5_ATAC-Seq |
| Sample type |
SRA |
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| Source name |
control thoracic motor neurons replicate 2
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| Organism |
Mus musculus |
| Characteristics |
tissue: thoracic motor neurons
genotype: control
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from purified dissected mouse embryonic MNs. Cells were aliquoted and washed twice in ice-cold 1× PBS. Cell pellets were resuspended in 10 mM Tris (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 (v/v), 0.1% tween20, 0.01% Digitonin and 1% BSA, centrifuged at 500 g for 5 min at 4°C. Pellets were resuspended in 12.5 ul of 2× tagmentation DNA buffer, 1.25 ul Tn5 (Nextera DNA Sample Preparation Kit, FC-121€“1030) and 11.25 ul of water, and incubated at 37°C for 30 min. The sample was purified using the MinElute PCR Purification Kit (Qiagen, 28004). PCR enrichment of the library was performed with custom-designed primers and 2× NEB Master Mix. A qPCR reaction with 1× SYBR Green (Invitrogen), custom-designed primers and 2× NEB Master Mix (New England Labs, M0541) was performed to determine the optimal number of PCR cycles (one third of the maximum measured fluorescence) (Buenrostro et al., 2013). The libraries were purified using the AMPure XP beads (Beckman Coulter, A63880). High Sensitivity DNA ScreenTape (Agilent, 5067-5584) was used to verify the fragment length distribution of the library. Library quantification was performed using the KAPA Library Amplification kit on a Roche LightCycler 480. The libraries were sequenced on an Illumina NovaSeq (100 cycles, paired-end)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and ATAC-Seq reads were mapped using bowtie2
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
ATAC-Seq peak calling was performed using MACS
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (.bw), Count Tables (.txt)
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| Submission date |
May 25, 2021 |
| Last update date |
Jan 10, 2022 |
| Contact name |
Alireza Khodadadi-Jamayran |
| Organization name |
New York University, NYU Langone Medical Center
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| Department |
Division of Advanced Research Technologies (DART)
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| Lab |
Applied Bioinformatics Laboratories (ABL)
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| Street address |
550 1st Ave, MSB 304
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| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE175503 |
PRC1 Sustains the Memory of Neuronal Fate Independent of PRC2 Function |
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| Relations |
| BioSample |
SAMN19328810 |
| SRA |
SRX10978074 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5335565_19-T4_S5_RPM.bw |
675.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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