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| Status |
Public on Dec 20, 2022 |
| Title |
Labelling transcriptional response to dissociation using SLAMseq |
| Organisms |
Danio rerio; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set
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| Overall design |
10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. A 4sU injected control was added to the zebrafish samples to identify high turnover genes
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| Contributor(s) |
Neuschulz A, Badillo-Lisakowski V, Gomez-Argente I |
| Citation(s) |
36573354 |
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| Submission date |
May 12, 2022 |
| Last update date |
Mar 22, 2023 |
| Contact name |
Anika Neuschulz |
| Organization name |
Max-Delbrück-Center for Molecular Medicine
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| Lab |
Junker
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| Street address |
Hannoversche Strasse 28
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| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (26)
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| GSM6135015 |
adult cardiomyocytes, no 4sU, rep2 |
| GSM6135016 |
prenatal cardiomyocytes, 30min 4sU, rep1 |
| GSM6135017 |
prenatal cardiomyocytes, 30min 4sU, rep2 |
| GSM6135018 |
prenatal cardiomyocytes, 30min 4sU, rep3 |
| GSM6135019 |
mESC, 2h, 100uM |
| GSM6135020 |
mESC, 6h, 100uM |
| GSM6135021 |
mESC, 24h, 100uM |
| GSM6135022 |
mESC, 2h, 1mM |
| GSM6135023 |
mESC, 6h, 1mM |
| GSM6135024 |
mESC, 24h, 1mM |
| GSM6135025 |
mESC, 2h, 10mM |
| GSM6135026 |
mESC, 6h, 10mM |
| GSM6135027 |
mESC, 24h, 10mM |
| GSM6135028 |
larvae, dissociated |
| GSM6135029 |
larvae, injected |
| GSM6135030 |
larvae, homogenized |
| GSM6735812 |
adult cardiomyocytes, 30 min 4sU, rep3 |
| GSM6735813 |
adult cardiomyocytes, 30 min 4sU, rep4 |
| GSM6735814 |
adult cardiomyocytes, 30 min 4sU, rep5 |
| GSM6735815 |
mESC, 24h, 0uM |
| GSM6735816 |
larvae, cold dissociated, rep 1 |
| GSM6735817 |
larvae, cold dissociated, rep 2 |
| GSM6735818 |
larvae, cold dissociated, rep 3 |
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| This SubSeries is part of SuperSeries: |
| GSE202949 |
Measuring stress response upon tissue dissociation using SLAMseq in bulk and single cells |
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| Relations |
| BioProject |
PRJNA837586 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE202880_RAW.tar |
15.8 Mb |
(http)(custom) |
TAR (of TSV, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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