Back

In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia

Bakina, O.; Conrad, T.; Mitic, N.; Vidal, R. O.; Obrusnik, T.; Sai, S.; Nolte, C.; Semtner, M.; Kettenmann, H.

2023-03-25 immunology
10.1101/2023.03.22.533782 bioRxiv
Show abstract

We applied the patch-seq technique to harvest transcripts from individual microglial cells from cortex, hippocampus and corpus callosum of acute brain slices from adult mice. After recording membrane currents with the patch-clamp technique, the cytoplasm was collected via the pipette and underwent adapted SMART-seq2 preparation with subsequent sequencing. On average, 4138 genes were detected in 113 cells from hippocampus, corpus callosum and cortex, including microglia markers such as Tmem119, P2ry12 and Siglec-H. Comparing our dataset to previously published single cell mRNA sequencing data from FACS-isolated microglia indicated that two clusters of cells were absent in our patch-seq dataset. Pathway analysis of marker genes in FACS-specific clusters revealed association with microglial activation and stress response. This indicates that under normal conditions microglia in situ lack transcripts associated with a stress-response, and that the microglia-isolation procedure by mechanical dissociation and FACS triggers the expression of genes related to activation and stress.

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
Brain, Behavior, and Immunity
○ 116 papers in training set
Top 0.1%
26.0%
Similar papers in this journal
2
Journal of Neuroinflammation
○ 61 papers in training set
Top 0.1%
12.6%
Similar papers in this journal
3
eLife
● 5828 papers in training set
Top 23%
5.4%
Similar papers in this journal
4
Glia
○ 81 papers in training set
Top 0.3%
5.4%
Similar papers in this journal
5
Life Science Alliance
● 285 papers in training set
Top 0.9%
3.9%
50% of probability mass above
6
iScience
○ 1154 papers in training set
Top 5%
3.9%
Similar papers in this journal
7
Scientific Reports
○ 3612 papers in training set
Top 26%
3.9%
8
BMC Biology
○ 265 papers in training set
Top 0.6%
3.4%
9
Frontiers in Immunology
○ 638 papers in training set
Top 4%
3.1%
10
Cell Reports
○ 1498 papers in training set
Top 14%
2.6%
11
Journal of Neurochemistry
○ 53 papers in training set
Top 0.4%
2.4%
12
Communications Biology
○ 993 papers in training set
Top 11%
2.1%
13
Frontiers in Cellular Neuroscience
○ 91 papers in training set
Top 1%
1.5%
14
EMBO Reports
○ 263 papers in training set
Top 4%
1.5%
15
PLOS Biology
● 486 papers in training set
Top 7%
1.3%
16
European Journal of Immunology
○ 60 papers in training set
Top 1%
1.1%
17
Cells
○ 249 papers in training set
Top 6%
1.0%
18
The FASEB Journal
○ 194 papers in training set
Top 5%
1.0%
19
Frontiers in Cell and Developmental Biology
○ 233 papers in training set
Top 4%
1.0%
20
eneuro
● 439 papers in training set
Top 7%
0.9%
21
International Journal of Molecular Sciences
○ 494 papers in training set
Top 16%
0.8%
22
Biosensors and Bioelectronics
○ 57 papers in training set
Top 0.8%
0.8%
23
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 42%
0.8%
24
Acta Neuropathologica Communications
○ 89 papers in training set
Top 2%
0.6%
25
Brain, Behavior, & Immunity - Health
○ 28 papers in training set
Top 0.7%
0.6%
26
Journal of Cell Science
● 393 papers in training set
Top 5%
0.6%
27
Nature Communications
○ 5641 papers in training set
Top 60%
0.6%
28
BMC Genomics
○ 406 papers in training set
Top 9%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.