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| Status |
Public on Jun 23, 2024 |
| Title |
JCB-5 E12.5 GFP- GFP |
| Sample type |
SRA |
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| Source name |
hindbrain
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| Organism |
Mus musculus |
| Characteristics |
tissue: hindbrain
strain: C57BL/6
antibody: GFP (Rabbit monoclonal, Invitrogen, G10362; 1:1000)
age: E12.5
genotype: Atoh1 GFP/GFP
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The hindbrains of 28 E12.5 and 24 E14.5 Atoh1GFP/GFP embryos were dissected in ice-cold HEBG media (0.8X B27, 0.25X GlutaMAX in Hibernate E media). Tissues were incubated with Worthington Papain solution at 37°C for 30 min at 800 rpm. At the end of incubation, the samples were transferred to 15 mL falcon tube, followed by gentle trituration with serologic pipette. The cell pellets were collected by centrifuge at 200 rcf for 3 min at 4°C, washed and resuspended in ice-cold sorting buffer (PBS with 0.05% fetal bovine serum). The single-cell resuspension was loaded to 30 µm cell drainer to remove debris, followed by DAPI staining at RT for 5 min. GFP+DAPI- and GFP-DAPI- cells were sorted by Sony SH800S. CUT&RUN was then performed on 200,000 sorted cells with an anti-GFP antibody and IgG antibody for each sample.
Following protocols.IO (dx.doi.org/10.17504/protocols.io.bagaibse) using NEB Next Ultra II DNA Library Prep Kit (E7645S) and NEB Unique Combinatorial Dual index kit (E6442S)
Sequencing at GENEWIZ using Illumina Novaseq S2 lane with 150bp PE reads
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Adapter trimming with Trimmomatic version 0.36 (2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25) and kseq
Alignment was performed with bowtie2-2.3.4.1 (--dovetail --phred33)
samtools (1.10) used to isolate fragmnets <120bp (for CIC and IgG) and generate BAM files
Bedtools (v2.29.1) was used to process BAM files to BED files, remove blacklist, and generate bigwigs.
Bedtools (v2.29.1) was used to merge replicate BAM files together for peak calling
Peaks called using MACSr (version 1.00, macs3 callpeak parameters “BAMPE”, qvalue = 0.05)
Assembly: mm10 (GRCm38 GCA_000001635.2) and the spike in Ecoli K12 Genomes (GCF_000005845.2_ASM584v2)
Supplementary files format and content: BW
Library strategy: CUT&RUN
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| Submission date |
Jun 02, 2023 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Huda Zoghbi |
| E-mail(s) |
hzoghbi@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Street address |
1250 Moursund St
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| City |
Houston |
| State/province |
Tx |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE233964 |
A single cell transcriptomic map of the developing Atoh1-lineage uncovers neural fate decisions and neuronal diversity in the hindbrain. [CUT&RUN] |
| GSE233966 |
A single cell transcriptomic map of the developing Atoh1-lineage uncovers neural fate decisions and neuronal diversity in the hindbrain. |
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| Relations |
| BioSample |
SAMN35577657 |
| SRA |
SRX20585161 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7439878_JCB-5.notsorted_120.SpikeInNormalized.bw |
64.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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