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| Status |
Public on Nov 23, 2023 |
| Title |
E45_Bla_CDX2_CR_rep2 |
| Sample type |
SRA |
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| Source name |
E4.5 blatocyst
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| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
strain: mix
antibody: Cdx2 (CST, 12306)
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| Growth protocol |
For collection of wildtypes E4.25 blastocyst, 4–6-week-old female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with malemice. E4.25 blastocyst were flushed out from the uterus at E4.25.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells or embyos were lysed in wash buffer.
CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ for 3-5 hours on a thermomixer at 400 rpm. After washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 1 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2 × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
library strategy: CUT&RUN
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq tracks, gene expression table for RNA-seq data
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| Submission date |
Oct 20, 2022 |
| Last update date |
Nov 23, 2023 |
| Contact name |
Lijia Li |
| E-mail(s) |
lijiali1119@gmail.com
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| Organization name |
Tsinghua University
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| Department |
School of Life Science
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| Lab |
Wei Xie lab
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| Street address |
Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE216256 |
Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos |
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| Relations |
| BioSample |
SAMN31394237 |
| SRA |
SRX17979246 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6664861_E45_Bla_CDX2_CR_rep2.bw |
62.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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