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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 15, 2024 |
| Title |
Hnrnpk is essential for embryonic limb bud development as a transcription activator and insulator collaborator |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Proper development of limb bud relies on the concordance of various signals, otherwise limb deformities occur. We report that heterogeneous nuclear ribonucleoprotein K (hnRNPK) is essential for limb bud development. here, we knock out Hnrnpk in limb bud and exert the RNA-seq, ATAC-seq, CUT&RUN-seq, and Hi-C assay using primary limb bud cells to explore the function of Hnrnpk in limb bud development.
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| Overall design |
ATAC-seq, mRNA, Ctcf binding, Hnrnpk binding, H3K4me1 binding, H3K4me3 binding and HiC profile of mice limb bud cells with or without Hnrnpk
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| Contributor(s) |
Chen Y, Zhou T |
| Citation(s) |
37608075 |
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| Submission date |
Oct 22, 2021 |
| Last update date |
Apr 16, 2024 |
| Contact name |
Yuyu Chen |
| E-mail(s) |
chenyy225@mail2.sysu.edu.cn
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| Phone |
+8618819473165
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| Organization name |
Sun Yat-sen University
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| Street address |
Zhongshan II road, 74th
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510080 |
| Country |
China |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (34)
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| GSM5651296 |
CKO Rep1 for RNA-seq |
| GSM5651297 |
CKO Rep2 for RNA-seq |
| GSM5651298 |
CKO Rep3 for RNA-seq |
| GSM5651299 |
WT Rep1 for ATAC-seq |
| GSM5651300 |
WT Rep2 for ATAC-seq |
| GSM5651301 |
WT Rep3 for ATAC-seq |
| GSM5651302 |
CKO Rep1 for ATAC-seq |
| GSM5651303 |
CKO Rep2 for ATAC-seq |
| GSM5651304 |
CKO Rep3 for ATAC-seq |
| GSM5651305 |
WT for CUT&RUN using Hnrnpk |
| GSM5651306 |
WT for CUT&RUN using Ctcf |
| GSM5651307 |
CKO for CUT&RUN using Ctcf |
| GSM5651308 |
WT for CUT&RUN using H3K4me1 |
| GSM5651309 |
CKO for CUT&RUN using H3K4me1 |
| GSM5651310 |
WT for CUT&RUN using H3K4me3 |
| GSM5651311 |
CKO for CUT&RUN using H3K4me3 |
| GSM5651312 |
WT for HiC |
| GSM5651313 |
CKO for HiC |
| GSM6205545 |
WT for CUT&RUN using Ctcf, Rep1 |
| GSM6205546 |
WT for CUT&RUN using Ctcf, Rep2 |
| GSM6205547 |
CKO for CUT&RUN using Ctcf, Rep1 |
| GSM6205548 |
CKO for CUT&RUN using Ctcf, Rep2 |
| GSM6205549 |
WT for CUT&RUN using H3K4me1, Rep1 |
| GSM6205550 |
WT for CUT&RUN using H3K4me1, Rep2 |
| GSM6205551 |
CKO for CUT&RUN using H3K4me1, Rep1 |
| GSM6205552 |
CKO for CUT&RUN using H3K4me1, Rep2 |
| GSM6205553 |
WT for CUT&RUN using H3K4me3, Rep1 |
| GSM6205554 |
WT for CUT&RUN using H3K4me3, Rep2 |
| GSM6205555 |
CKO for CUT&RUN using H3K4me3, Rep1 |
| GSM6205556 |
CKO for CUT&RUN using H3K4me3, Rep2 |
| GSM7081149 |
WT Rep2 for CUT&RUN using Hnrnpk |
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| Relations |
| BioProject |
PRJNA773754 |
| SRA |
SRP342717 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE186411_RAW.tar |
9.8 Gb |
(http)(custom) |
TAR (of BW, HIC) |
| GSE186411_ZTF_mRNA-seq.fpkm.mrna.ann.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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