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Raw scRNA-seq FASTQ data files for: Nerve growth factor responsive elements modulate immune cell inflammation and are dysregulated in an Alzheimer's disease mouse model

https://doi.org/10.48723/d5mw-0122
This dataset contains raw single-cell RNA sequencing (scRNA-seq) FASTQ files generated from splenocytes isolated from wild-type C57BL/6J mice (n = 2). Libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 and sequenced on an Illumina NextSeq 2000 platform. The dataset consists of paired-end raw sequencing files associated with a study titled "Nerve growth factor responsive elements modulate immune cell inflammation and are dysregulated in an Alzheimer's disease mouse model". The dataset consists of four (4) files: - RGAD_WT_S1_L001_R1_001.fastq.gz Forward reads for WT sample 1 - RGAD_WT_S1_L001_R2_001.fastq.gz Reverse reads for WT sample 1 - RGAD_WT1_S1_L001_R1_001.fastq.gz Forward reads for WT sample 2 - RGAD_WT1_S1_L001_R2_001.fastq.gz Reverse reads for WT sample 2
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Data files

Documentation files

Citation and access

Data access level:

Creator/​Principal investigator(s):

Research principal:

Data contains personal data:

No

Citation:

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Method and outcome

Unit of analysis:

Population:

Wild-type Mus musculus C57BL/6J laboratory mice; splenocyte-derived single-cell suspensions used for scRNA-seq analysis.

Study design:

  • Experimental study
  • Preclinical study

Description of study design:

Preclinical experimental study involving wild-type C57BL/6J mice. Splenocytes were isolated and processed for single-cell RNA sequencing (scRNA-seq) to generate transcriptomic profiling data. Sequencing platform: Illumina NextSeq 2000 Library preparation: 10x Genomics Chromium Next GEM Single Cell 3′ Reagent Kit v3.1

Description of sampling:

2 biological samples

Data format/​data structure:

Data collection Laboratory experiment

Mode of collection:

Laboratory experiment

Description of the mode of collection:

Mice were kept on a 12h light/dark cycle and food and water were available ad libitum. Mice were deeply anesthetized using isoflurane to collect spleen. Dissected spleens were processed to collect splenic immune cells. After isolation, the splenocytes were counted and the viability was measured with the Luna FL dual fluorescence cell counter with dual stain Acridine Orange/Propidium Iodide, with cell size gated between 1-60 μm (Logos Biosystems). Cell suspensions with viability of 85% were encapsulated using the Next Gem Single Cell 3′ Reagent kit v3.1. (Dual index) from 10x Genomics (cat: PN-100026), aiming to capture 5,000 cells. Libraries were prepared as per manufacturer’s instruction (protocol CG000315) and sequenced using the Illumina platform on a Next seq2000 P3 100 cycles flow cell, aiming for an average read depth of 40,000 reads/cell. The cell capture and library generation were performed at the Single Cell Core Facility of Flemingsberg Campus (SICOF) that receives funding from the Infrastructure Board at Karolinska Institutet.

Instrument

Name:

Illumina NextSeq 2000

Type:

Technical instrument(s)

Administrative information

Responsible department/​unit:

Department of Neurobiology, Care Sciences and Society [H1]

Ethics Review 1:

Stockholm - 12.570–2021

Stockholm Animal Ethical Committee

Ethics Review 2:

Stockholm - 5406–2020

Stockholm Animal Ethical Committee

Ethics Review 3:

Linköping - ID 407

Linköping Animal Ethical Committee

Topic and keywords

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Standard för svensk indelning av forskningsämnen 2025:

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Metadata

Version 1
doris
ki
Published: