 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 30, 2023 |
| Title |
E12.5 mouse embryonic maxillary prominence_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
maxillary prominence
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: embryo 12.5
genotype: wild type
|
| Treatment protocol |
On Embryo 10.5(E10.5), 11.5, or 12.5, pregnant C57BL/6 female were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope and used for library construction as described below.
|
| Growth protocol |
C57BL/6 mice were purchased from Shanghai Jihui Laboratory Animal Care Co.Ltd. All mice were maintained in SPF conditions at the Animal Center of the Ninth People’s hospital affiliated to Shanghai Jiaotong University School of medicine. Female and male mice between the ages of 8 to 12 weeks were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol from freshly dissected maxillary prominence tissues from 7 littermates. For each developmental stage (E10.5, E11.5 and E12.5), three independent RNA samples were prepared. RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For each sample, 2 μg total RNA was used as input material for the library preparations. Sequencing libraries were then generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and eluted with EB buffer, followed by terminal repair, A-tailing and adapter ligation. The ligated products were retrieved and PCR amplification was performed to generate sequencing libraries. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurately quantified using a StepOnePlusTM Real-Time PCR System. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina HiSeq X ten platform and 150 bp paired-end reads were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The PE150 raw reads of RNA-Seq libraries were filtered by removing adaptor sequences, contamination and low-quality (phred quality < 20) reads. Reads quality was assessed using FastQC.
Sequenced reads were then mapped to the mm10 genome using STAR aligner version 2.7.3a. Reads were counted using htseq-count version 0.12.4 at the union mode.
|
| |
|
| Submission date |
Nov 09, 2020 |
| Last update date |
Nov 30, 2023 |
| Contact name |
Jian Sun |
| E-mail(s) |
orthodoc_sun@hotmail.com
|
| Phone |
021-15821965892
|
| Organization name |
Shanghai Ninth People's Hospital
|
| Street address |
Quxi Road No.500
|
| City |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE161126 |
Single-cell transcriptome profiling reveals developmental trajectory and regulatory networks of mouse maxillary prominence [RNA-seq] |
| GSE161131 |
Single-cell transcriptome profiling reveals developmental trajectory and regulatory networks of mouse maxillary prominence |
|
| Relations |
| BioSample |
SAMN16709965 |
| SRA |
SRX9463106 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4889932_E12.5-3.counts.txt.gz |
194.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
