TRAP-SEQ (Translating Ribosome Affinity Purification followed by RNA sequencing) of iBAT-related ganglia from 7-day cold and warm treated mice

Heike Muenzberg, Ph.D.
Michael Salbaum
Hans-Rudolf Berthoud
Sangho Yu
rui zhang, Ph.D.
Clara Huesing, Ph.D.
Nathan Lee, B.S.
Richard Carmouche
Sara Webb
Susan Newman

Molecular-genetic techniques in the autonomic nervous system: Projection-specific tracing and ribosomal RNA pulldown

Updated on May 13, 2021 (Version 1)

Corresponding Contributor:

Heike Muenzberg
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Dataset Overview

Study purpose: The study goal is to identify the gene expression profile of the interscapular brown adipose tissue, iBAT-related postganglionic neurons in the 7-day cold and warm treated conditions by looking for genes that are enriched in the IP samples, when comparing to the input samples.

Data collection: RNA sequencing raw data in fastq, bz2 files.

Primary conclusion: We have generated a large cohort of L10-EGFP mice for viral injections which will generate new samples with pooled ganglia tissue from 4 animals (2 Males, 2 Females). We confirmed good GFP enrichment in our samples, and were overall able to show enriched genes. However, we find many variations across samples, and the quality of RNA pulldown is not fully satisfactory, possibly due to low RNA recovery. Sample pooling and pulldown efficiency will need further optimization, even though our data verify that this method is overall feasible.

Curator's Notes

Experimental Design: Sympathetic ganglia SG/T1-T5 were isolated from 32 L10EGFP mice (RRID:IMSR_JAX:024750). The mice (16 males and 16 females) were injected with AAV6-hSyn-mCherry-cre in interscapular brown adipose tissue bilaterally, iBAT, followed by about 4 weeks incubation. Then 16 mice (8 males and 8 females) were treated with cold room temperature (10 °C) for 7 days and another group of 16 mice were treated with warm room temperature (28 °C) for 7 days. TRAP method was used for extracting and purifying iBAT related mRNA in stellate ganglia/T1-T5 (ganglia from 2 males and 2 females were combined as one sample for both cold treatment and warm treatment groups). 16 pool samples were analyzed.

Completeness: This dataset is a part of a larger study: "Genetically-based neuro-modulation of adipose tissue functions".

Subjects & Samples: Female (n=16) and male (n=16) adult mice (RRID:IMSR_JAX:024750) 17-31 weeks old were used in this study.

Primary vs derivative data: Primary data consists of raw sequencing data in fastq, bz2 files organized in pooled sample ID folders. Information about related samples and pooling schema can be found in sample metadata file. There is no derivative data.

Important Notes: This dataset is currently undergoing image registration and will be updated once this process is complete.


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Publishing history

May 13, 2021
Originally Published
May 13, 2021 (Version 1)
Last Updated

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