title: rrbs_hippoc_control_male_8w_biological_rep2_vial_90229015203


title: rrbs_hippoc_control_female_8w_biological_rep3_vial_90252015203

status: Public on Sep 30 2023

type: SRA

city: Stanford

first: Euan

last: Ashley

state: CA

address: 870 Quarry Road

country: USA

institute: Stanford University

library_source: genomic

data_processing:
Reads were demultiplexed with bcl2fastq (version 2.20) using options --use-bases-mask Y*,I8Y*,I*,Y* --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0 (Illumina, San Diego, CA, USA), and UMIs in the index FASTQ files were attached to the read FASTQ files
The regular 5-prime and 3-prime adapters were trimmed with TrimGalore (v1.18), and the diversity adapter that is about 0 to 3 bases of RDD (R={A or G} and D={A, G, or T}) that is added before YGG (Y={C or T} depending on the methylation) from the YGG MspI cut signature was trimmed with the NuGEN script trimRRBSdiversityAdaptCustomers.py (https://github.com/nugentechnologies/NuMetRRBS)
FastQC (v0.11.8) was used to generate pre-alignment QC metrics3
Bismark (v0.20.0) was used to index and align reads to release 96 of the Ensembl Rattus norvegicus (rn6) genome and gene annotation
As the lambda genome was spiked into each sample to determine the bisulfite conversion efficiency, the lambda genome (GenBank: J02459.1) was also indexed
Default parameters were used for Bismark's  bismark_genome_preparation in the alignment step
Bismark output BAM files were first formatted using a custom script; Bismark's deduplicate_bismark with -p --barcode options was used to remove PCR duplicates from the bam files; and Bismark's bismark_methylation_extractor --comprehensive --bedgraph was used to quantify methylated and unmethylated coverages for all the CpG sites
Bowtie 2 (v2.3.4.3) was used to index and align reads to globin, rRNA, and phix sequences in order to quantify the percent of reads that mapped to these contaminants and spike-ins
SAMtools (v1.3.1) was used to compute mapping percentages to different chromosomes
UMIs were used to accurately quantify PCR duplicates with NuGEN's nodup.py script (https://github.com/tecangenomics/nudup)
QC metrics from every stage of the quantification pipeline were compiled, in part with multiQC (v1.6)
The openWDL-based implementation of the RRBS pipeline on Google Cloud Platform is available on GitHub (https://github.com/MoTrPAC/motrpac-rrbs-pipeline).
Assembly: rn6
Supplementary files format and content: Methylated and unmethylated coverages across all CpG sites for the species aligned sample. One file per sample/tissue. Available through command-line only. Table format : <chr> <start> <end><methylation percentage> <count methylated> <count unmethylated>

molecule: genomic DNA

organism: Rattus norvegicus

source_name: RRBS of Rat Female Hippocampus Powder Control - 8 weeks

extract_protocol:
Reduced representation bisulfite sequencing (RRBS)2 was performed at the Icahn School of Medicine at Mount Sinai. Rat tissues (10-30 mg of white adipose tissue) were disrupted in GenFind v2 lysis buffer (Beckman Coulter, Indianapolis, IN) using a tissue ruptor (Omni International, Kennesaw, GA) and the genomic DNA was extracted in a BiomekFx automation workstation (Beckman Coulter, Chaska, Minnesota), according to the manufacturerΓÇÖs instructions. Two tissue-specific consortium reference standards were included to monitor the sample processing QC. DNA samples were quantified by Qubit assay (dsDNA HR assay, Thermo Fisher Scientific), and the quality was determined by the Nanodrop A260/280 and A260/230 ratios.
The Ovation RRBS Methyl-Seq kit from Tecan Genomics (Baldwin Park, CA) was used to generate the RRBS libraries according to the manufacturer's instructions. All library preparations were carried out in an automated workstation (Biomek Fx, Beckman Coulter). Briefly, purified genomic DNA (100 ng) was digested by the methylation-insensitive restriction enzyme MspI to generate short fragments that contain CpG dinucleotides at the ends. After end-repair, A-tailing, and ligation to methylated Illumina adapters, the CpG-rich DNA fragments (40-220 base pairs) were size-selected and subjected to bisulfite conversion according to the manufacturer's instructions. The single-stranded uracil-containing DNA was purified after desulfonation using the magnetic beads provided in the kit, and eluted DNA was converted to double-stranded DNA by PCR with the following cycling parameters: 95C for 2 minutes, followed by the optimal number of cycles of 95C for 15 seconds, 60C for 1 minute, and 72C for 30 seconds, and a final step at 72C for 10 minutes. The optimal number of cycles for the enrichment PCR was calculated based on qPCR values. A final clean-up step was performed by 1x AMPure XP beads. The quantity of the libraries was measured by Qubit High Sensitivity assays (ThermoFisher Scientific), and the quality was evaluated using Bioanalyzer High Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA). The libraries were pooled and 10 sequenced in a MiSeq Nano flow cell to determine the sequencing quality of the libraries. Unmethylated lambda DNA (Promega, D1521) was spiked (0.05%) in each sample to monitor bisulfite conversion. Jurkat genomic DNA (ThermoFisher, SD1111) and CpG Methylated Jurkat genomic DNA (ThermoFisher, SD1121) were used as positive controls with each batch.

tag: tissue

value: Hippocampus Powder

tag: treatment

value: Control - 8 weeks


title: rrbs_hippoc_control_male_8w_biological_rep3_vial_90232015203

source_name: RRBS of Rat Male Hippocampus Powder Control - 8 weeks


title: rrbs_hippoc_training_male_8w_biological_rep5_vial_90227015203

source_name: RRBS of Rat Male Hippocampus Powder Training - 8 weeks

value: Training - 8 weeks


title: rrbs_hippoc_training_male_8w_biological_rep4_vial_90225015203


title: rrbs_hippoc_training_male_8w_biological_rep2_vial_90222015203


title: rrbs_bat_female_reference_7_vial_80031996906

source_name: RRBS of Rat Female Brown Adipose Powder Reference

value: Brown Adipose Powder

value: Reference


title: rrbs_hippoc_training_male_4w_biological_rep1_vial_90280015203

source_name: RRBS of Rat Male Hippocampus Powder Training - 4 weeks

value: Training - 4 weeks


title: rrbs_bat_male_reference_7_vial_80030886906

source_name: RRBS of Rat Male Brown Adipose Powder Reference


title: rrbs_hippoc_training_female_8w_biological_rep1_vial_90251015203

source_name: RRBS of Rat Female Hippocampus Powder Training - 8 weeks


title: rrbs_wat_female_reference_8_vial_80005997013

source_name: RRBS of Rat Female White Adipose Powder Reference

value: White Adipose Powder


title: rrbs_hippoc_training_male_4w_biological_rep3_vial_90283015203


title: rrbs_hippoc_training_male_8w_biological_rep1_vial_90218015203


title: rrbs_hippoc_training_male_8w_biological_rep3_vial_90223015203


title: rrbs_lung_male_reference_5_vial_80026886617

source_name: RRBS of Rat Male Lung Powder Reference

value: Lung Powder


title: rrbs_liver_female_reference_6_vial_80003996807

source_name: RRBS of Rat Female Liver Powder Reference

value: Liver Powder


title: rrbs_wat_male_reference_8_vial_80004887013

source_name: RRBS of Rat Male White Adipose Powder Reference


title: rrbs_lung_female_reference_5_vial_80027996605

source_name: RRBS of Rat Female Lung Powder Reference


title: rrbs_liver_male_reference_6_vial_80002886807

source_name: RRBS of Rat Male Liver Powder Reference


title: rrbs_hippoc_control_male_8w_biological_rep1_vial_90217015203


title: rrbs_kidney_female_reference_4_vial_80029995910

source_name: RRBS of Rat Female Kidney Powder Reference

value: Kidney Powder


title: rrbs_heart_female_reference_3_vial_80033995807

source_name: RRBS of Rat Female Heart Powder Reference

value: Heart Powder


title: rrbs_heart_male_reference_3_vial_80032885807

source_name: RRBS of Rat Male Heart Powder Reference


title: rrbs_kidney_male_reference_4_vial_80028885910

source_name: RRBS of Rat Male Kidney Powder Reference


title: rrbs_skm-gn_male_reference_2_vial_80000885508

source_name: RRBS of Rat Male Gastrocnemius Powder Reference

value: Gastrocnemius Powder


title: rrbs_skm-gn_female_reference_2_vial_80001995508

source_name: RRBS of Rat Female Gastrocnemius Powder Reference


title: rrbs_hippoc_female_reference_1_vial_80035995208

source_name: RRBS of Rat Female Hippocampus Powder Reference


title: rna-seq_liver_training_male_4w_biological_rep5_vial_90292016803

description: motrpac_pass1b-06_t68-liver_transcript-rna-seq_rsem-genes-count.txt

library_source: transcriptomic

data_processing:
Pooled libraries were sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) to a target depth of 35 million read pairs (70 million paired-end reads) per sample using a paired-end 100 base pair run configuration
In order to capture the 8-base UMIs, libraries were sequenced using 16 cycles for the i7 index read and 8 cycles for the i5 index read
Reads were demultiplexed with bcl2fastq2 (v2.20.0) using options --use-bases-mask Y*,I8Y*,I*,Y* --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0 (Illumina, San Diego, CA, USA), and UMIs in the index FASTQ files were attached to the read FASTQ files
Adapters were trimmed with cutadapt (v1.18), and trimmed reads shorter than 20 base pairs were removed
FastQC (v0.11.8) was used to generate pre-alignment QC metrics
STAR (v2.7.0d) was used to index and align reads to release 96 of the Ensembl Rattus norvegicus (rn6) genome and gene annotation
Default parameters were used for STAR's genomeGenerate run mode; in STAR's alignReads run mode, SAM attributes were specified as NH HI AS NM MD nM, and reads were removed if they did not contain high-confidence collapsed splice junctions (--outFilterType BySJout)
RSEM (v1.3.1) was used to quantify transcriptome-coordinate-sorted alignments using a forward probability of 0.5 to indicate a non-strand-specific protocol
Bowtie 2 (v2.3.4.3) was used to index and align reads to globin, rRNA, and phix sequences in order to quantify the percent of reads that mapped to these contaminants and spike-ins
UCSC's gtfToGenePred was used to convert the rn6 gene annotation (GTF) to a refFlat file in order to run Picard CollectRnaSeqMetrics (v2.18.16) with options MINIMUM_LENGTH=50 and RRNA_FRAGMENT_PERCENTAGE=0.3
UMIs were used to accurately quantify PCR duplicates with NuGEN's nodup.py script (https://github.com/tecangenomics/nudup)
QC metrics from every stage of the quantification pipeline were compiled, in part with multiQC (v1.6)
The openWDL-based implementation of the RNA-Seq pipeline on Google Cloud Platform is available at https://github.com/MoTrPAC/motrpac-rna-seq-pipeline.
Assembly: rn6
Supplementary files format and content: Consolidated raw read count matrix for genes (RSEM program) of all samples run per tissue/phase.

molecule: total RNA

source_name: RNA-Seq of Rat Male Liver Powder Training - 4 weeks

extract_protocol:
RNA sequencing (RNA-Seq) was performed at Stanford University and the Icahn School of Medicine at Mount Sinai. Rat tissues (30 mg for white adipose, 15 mg for brown adipose, 10 mg for other solid tissues, and 0.47 ml blood) were disrupted in Agencourt RNAdvance tissue lysis buffer (Beckman Coulter, Brea, CA) using a tissue ruptor (Omni International, Kennesaw, GA, # 19-040E). Total RNA was extracted in a BiomekFx automation workstation according to the manufacturer's instructions for tissue-specific extraction. Total RNA from blood collected in PAXgene tubes (BD Biosciences, Franklin Lakes, NJ, # 762165) was extracted using the Agencourt RNAdvance blood specific kit (Beckman Coulter). Two tissue-specific consortium reference standards were included to monitor the sample processing QC. The RNA was quantified by NanoDrop (ThermoFisher Scientific, # ND-ONE-W) and Qubit assay (ThermoFisher Scientific), and the quality was determined by either Bioanalyzer or Fragment Analyzer analysis.
Universal Plus mRNA-Seq kit from NuGEN/Tecan (# 9133) were used for generation of RNA- Seq libraries derived from poly(A)-selected RNA according to the manufacturer's instructions. Universal Plus mRNA-Seq libraries contain dual (i7 and i5) 8 bp barcodes and an 8 bp unique molecular identifier (UMI), which enable deep multiplexing of NGS sequencing samples and accurate quantification of PCR duplication levels. Approximately 500ng of total RNA were used to generate the libraries. The Universal Plus mRNA-Seq workflow consists of poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mix-ture of random and oligo(dT) priming, end repair to generate blunt ends, adaptor ligation, strand selection, AnyDeplete workflow to remove unwanted ribosomal and globin transcripts, and PCR amplification to enrich final library species. All library preparations were performed using a 13 Biomek i7 laboratory automation system (Beckman Coulter). Tissue-specific reference standards provided by the consortium were included with all RNA isolations to QC the RNA.


title: rna-seq_liver_training_male_4w_biological_rep4_vial_90289016803


title: rna-seq_liver_training_male_4w_biological_rep3_vial_90283016803


title: rrbs_hippoc_male_reference_1_vial_80034885208

source_name: RRBS of Rat Male Hippocampus Powder Reference


title: rna-seq_liver_training_male_4w_biological_rep2_vial_90281016803


title: rna-seq_kidney_training_male_8w_biological_rep3_vial_90223015902

description: motrpac_pass1b-06_t59-kidney_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Male Kidney Powder Training - 8 weeks


title: rna-seq_liver_training_female_4w_biological_rep1_vial_90406016803

source_name: RNA-Seq of Rat Female Liver Powder Training - 4 weeks


title: rna-seq_kidney_control_male_8w_biological_rep1_vial_90217015902

source_name: RNA-Seq of Rat Male Kidney Powder Control - 8 weeks


title: rna-seq_heart_training_female_2w_biological_rep5_vial_90587015803

description: motrpac_pass1b-06_t58-heart_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Female Heart Powder Training - 2 weeks

value: Training - 2 weeks


title: rna-seq_venacv_training_female_4w_biological_rep5_vial_90420016502

description: motrpac_pass1b-06_t99-vena-cava_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Female Vena Cava Powder Training - 4 weeks

value: Vena Cava Powder


title: rna-seq_kidney_training_male_8w_biological_rep2_vial_90222015902


title: rna-seq_venacv_training_female_4w_biological_rep3_vial_90412016502


title: rna-seq_kidney_training_male_8w_biological_rep1_vial_90218015902


title: rna-seq_venacv_training_male_4w_biological_rep4_vial_90289016502

source_name: RNA-Seq of Rat Male Vena Cava Powder Training - 4 weeks


title: rna-seq_venacv_training_female_4w_biological_rep4_vial_90416016502


title: rna-seq_venacv_training_female_4w_biological_rep1_vial_90406016502


title: rna-seq_venacv_training_male_4w_biological_rep3_vial_90283016502


title: rna-seq_venacv_training_male_4w_biological_rep5_vial_90292016502


title: rna-seq_venacv_training_male_4w_biological_rep1_vial_90280016502


title: rna-seq_venacv_control_female_8w_biological_rep5_vial_90266016502

source_name: RNA-Seq of Rat Female Vena Cava Powder Control - 8 weeks


title: rna-seq_venacv_training_male_4w_biological_rep2_vial_90281016502


title: rna-seq_venacv_training_female_8w_biological_rep5_vial_90267016502

source_name: RNA-Seq of Rat Female Vena Cava Powder Training - 8 weeks


title: rna-seq_venacv_control_female_8w_biological_rep4_vial_90265016502


title: rna-seq_venacv_training_female_8w_biological_rep4_vial_90259016502


title: rna-seq_venacv_control_female_8w_biological_rep3_vial_90252016502


title: rna-seq_venacv_training_female_8w_biological_rep3_vial_90258016502


title: rna-seq_venacv_training_female_8w_biological_rep2_vial_90254016502


title: rna-seq_venacv_control_female_8w_biological_rep2_vial_90248016502


title: rna-seq_venacv_training_female_8w_biological_rep1_vial_90251016502


title: rna-seq_venacv_control_male_8w_biological_rep2_vial_90229016502

source_name: RNA-Seq of Rat Male Vena Cava Powder Control - 8 weeks


title: rna-seq_venacv_control_male_8w_biological_rep3_vial_90232016502


title: rna-seq_venacv_control_male_8w_biological_rep4_vial_90237016502


title: rna-seq_venacv_training_male_8w_biological_rep5_vial_90227016502

source_name: RNA-Seq of Rat Male Vena Cava Powder Training - 8 weeks


title: rna-seq_venacv_training_male_8w_biological_rep4_vial_90225016502


title: rna-seq_venacv_control_female_8w_biological_rep1_vial_90245016502


title: rna-seq_venacv_control_male_8w_biological_rep1_vial_90217016502


title: rna-seq_venacv_training_male_8w_biological_rep3_vial_90223016502


title: rna-seq_venacv_training_male_8w_biological_rep1_vial_90218016502


title: rna-seq_venacv_training_male_8w_biological_rep2_vial_90222016502


title: rna-seq_wat_training_female_2w_biological_rep5_vial_90587017005

description: motrpac_pass1b-06_t70-white-adipose_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Female White Adipose Powder Training - 2 weeks


title: rna-seq_wat_training_female_2w_biological_rep2_vial_90578017005


title: rna-seq_wat_training_female_1w_biological_rep5_vial_90571017005

source_name: RNA-Seq of Rat Female White Adipose Powder Training - 1 week

value: Training - 1 week


title: rna-seq_wat_training_female_1w_biological_rep4_vial_90567017005


title: rna-seq_wat_training_female_2w_biological_rep3_vial_90581017005


title: rna-seq_wat_training_female_2w_biological_rep1_vial_90576017005


title: rna-seq_wat_training_female_1w_biological_rep3_vial_90564017005


title: rna-seq_wat_training_female_2w_biological_rep4_vial_90585017005


title: rna-seq_wat_training_female_1w_biological_rep1_vial_90559017005


title: rna-seq_wat_training_female_1w_biological_rep2_vial_90560017005


title: rna-seq_wat_training_male_2w_biological_rep5_vial_90450017005

source_name: RNA-Seq of Rat Male White Adipose Powder Training - 2 weeks


title: rna-seq_wat_training_male_2w_biological_rep1_vial_90439017005


title: rna-seq_wat_training_male_1w_biological_rep5_vial_90430017005

source_name: RNA-Seq of Rat Male White Adipose Powder Training - 1 week


title: rna-seq_wat_training_male_2w_biological_rep4_vial_90449017005


title: rna-seq_wat_training_male_2w_biological_rep2_vial_90441017005


title: rna-seq_wat_training_male_2w_biological_rep3_vial_90444017005


title: rna-seq_wat_training_female_4w_biological_rep5_vial_90420017005

source_name: RNA-Seq of Rat Female White Adipose Powder Training - 4 weeks


title: rna-seq_venacv_training_female_4w_biological_rep2_vial_90410016502


title: rna-seq_wat_training_female_4w_biological_rep3_vial_90412017005


title: rna-seq_wat_training_female_4w_biological_rep2_vial_90410017005


title: rna-seq_wat_training_male_1w_biological_rep4_vial_90426017005


title: rna-seq_wat_training_male_4w_biological_rep5_vial_90292017005

source_name: RNA-Seq of Rat Male White Adipose Powder Training - 4 weeks


title: rna-seq_wat_training_male_1w_biological_rep1_vial_90421017005


title: rna-seq_wat_training_male_1w_biological_rep2_vial_90422017005


title: rna-seq_wat_training_male_4w_biological_rep4_vial_90289017005


title: rna-seq_wat_training_male_1w_biological_rep3_vial_90423017005


title: rna-seq_wat_training_male_4w_biological_rep2_vial_90281017005


title: rna-seq_wat_training_female_4w_biological_rep1_vial_90406017005


title: rna-seq_wat_training_male_4w_biological_rep1_vial_90280017005


title: rna-seq_wat_training_male_4w_biological_rep3_vial_90283017005


title: rna-seq_wat_control_female_8w_biological_rep5_vial_90266017005

source_name: RNA-Seq of Rat Female White Adipose Powder Control - 8 weeks


title: rna-seq_wat_control_female_8w_biological_rep4_vial_90265017005


title: rna-seq_wat_training_female_8w_biological_rep5_vial_90267017005

source_name: RNA-Seq of Rat Female White Adipose Powder Training - 8 weeks


title: rna-seq_venacv_control_male_8w_biological_rep5_vial_90239016502


title: rna-seq_wat_control_female_8w_biological_rep3_vial_90252017005


title: rna-seq_wat_training_female_8w_biological_rep3_vial_90258017005


title: rna-seq_wat_training_female_8w_biological_rep4_vial_90259017005


title: rna-seq_wat_training_female_8w_biological_rep2_vial_90254017005


title: rna-seq_wat_training_female_8w_biological_rep1_vial_90251017005


title: rna-seq_wat_control_female_8w_biological_rep2_vial_90248017005


title: rna-seq_wat_training_female_4w_biological_rep4_vial_90416017005


title: rna-seq_wat_control_female_8w_biological_rep1_vial_90245017005


title: rna-seq_wat_control_male_8w_biological_rep4_vial_90237017005

source_name: RNA-Seq of Rat Male White Adipose Powder Control - 8 weeks


title: rna-seq_wat_control_male_8w_biological_rep2_vial_90229017005


title: rna-seq_wat_control_male_8w_biological_rep5_vial_90239017005


title: rna-seq_wat_training_male_8w_biological_rep3_vial_90223017005

source_name: RNA-Seq of Rat Male White Adipose Powder Training - 8 weeks


title: rna-seq_wat_training_male_8w_biological_rep5_vial_90227017005


title: rna-seq_wat_training_male_8w_biological_rep2_vial_90222017005


title: rna-seq_wat_training_male_8w_biological_rep4_vial_90225017005


title: rna-seq_wat_training_male_8w_biological_rep1_vial_90218017005


title: rna-seq_bat_training_female_2w_biological_rep2_vial_90578016902

description: motrpac_pass1b-06_t69-brown-adipose_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Female Brown Adipose Powder Training - 2 weeks


title: rna-seq_wat_control_male_8w_biological_rep1_vial_90217017005


title: rna-seq_bat_training_female_1w_biological_rep4_vial_90567016902

source_name: RNA-Seq of Rat Female Brown Adipose Powder Training - 1 week


title: rna-seq_bat_training_female_2w_biological_rep5_vial_90587016902


title: rna-seq_bat_training_female_2w_biological_rep1_vial_90576016902


title: rna-seq_wat_control_male_8w_biological_rep3_vial_90232017005


title: rna-seq_bat_training_male_2w_biological_rep5_vial_90450016902

source_name: RNA-Seq of Rat Male Brown Adipose Powder Training - 2 weeks


title: rna-seq_bat_training_female_1w_biological_rep3_vial_90564016902


title: rna-seq_bat_training_female_1w_biological_rep1_vial_90559016902


title: rna-seq_bat_training_male_2w_biological_rep4_vial_90449016902


title: rna-seq_bat_training_female_1w_biological_rep2_vial_90560016902


title: rna-seq_bat_training_female_2w_biological_rep4_vial_90585016902


title: rna-seq_bat_training_male_2w_biological_rep1_vial_90439016902


title: rna-seq_bat_training_male_2w_biological_rep3_vial_90444016902


title: rna-seq_bat_training_male_2w_biological_rep2_vial_90441016902


title: rna-seq_bat_training_female_1w_biological_rep5_vial_90571016902


title: rna-seq_bat_training_male_1w_biological_rep4_vial_90426016902

source_name: RNA-Seq of Rat Male Brown Adipose Powder Training - 1 week


title: rna-seq_bat_training_male_1w_biological_rep5_vial_90430016902


title: rna-seq_bat_training_male_1w_biological_rep3_vial_90423016902


title: rna-seq_bat_training_male_1w_biological_rep1_vial_90421016902


title: rna-seq_bat_training_male_1w_biological_rep2_vial_90422016902


title: rna-seq_bat_training_female_4w_biological_rep5_vial_90420016902

source_name: RNA-Seq of Rat Female Brown Adipose Powder Training - 4 weeks


title: rna-seq_bat_training_female_4w_biological_rep4_vial_90416016902


title: rna-seq_bat_training_female_4w_biological_rep3_vial_90412016902


title: rna-seq_bat_training_male_4w_biological_rep5_vial_90292016902

source_name: RNA-Seq of Rat Male Brown Adipose Powder Training - 4 weeks


title: rna-seq_bat_training_female_4w_biological_rep1_vial_90406016902


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source_name: RNA-Seq of Rat Female Spleen Powder Training - 2 weeks

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title: rna-seq_testes_training_male_8w_biological_rep2_vial_90222016302


title: rna-seq_testes_training_male_8w_biological_rep3_vial_90223016302


title: rna-seq_testes_training_male_8w_biological_rep1_vial_90218016302


title: rna-seq_spleen_training_female_2w_biological_rep5_vial_90587016202


title: rna-seq_spleen_training_female_2w_biological_rep4_vial_90585016202


title: rna-seq_spleen_training_female_2w_biological_rep1_vial_90576016202


title: rna-seq_spleen_training_female_2w_biological_rep2_vial_90578016202


title: rna-seq_spleen_training_female_1w_biological_rep5_vial_90571016202

source_name: RNA-Seq of Rat Female Spleen Powder Training - 1 week


title: rna-seq_spleen_training_male_2w_biological_rep5_vial_90450016202

source_name: RNA-Seq of Rat Male Spleen Powder Training - 2 weeks


title: rna-seq_spleen_training_male_2w_biological_rep3_vial_90444016202


title: rna-seq_spleen_training_female_1w_biological_rep4_vial_90567016202


title: rna-seq_spleen_training_female_1w_biological_rep2_vial_90560016202


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title: rna-seq_spleen_training_male_2w_biological_rep4_vial_90449016202


title: rna-seq_spleen_training_female_1w_biological_rep1_vial_90559016202


title: rna-seq_spleen_training_female_1w_biological_rep3_vial_90564016202


title: rna-seq_spleen_training_male_1w_biological_rep4_vial_90426016202

source_name: RNA-Seq of Rat Male Spleen Powder Training - 1 week


title: rna-seq_spleen_training_male_1w_biological_rep5_vial_90430016202


title: rna-seq_spleen_training_male_1w_biological_rep3_vial_90423016202


title: rna-seq_spleen_training_female_4w_biological_rep5_vial_90420016202

source_name: RNA-Seq of Rat Female Spleen Powder Training - 4 weeks


title: rna-seq_spleen_training_male_1w_biological_rep1_vial_90421016202


title: rna-seq_spleen_training_male_1w_biological_rep2_vial_90422016202


title: rna-seq_spleen_training_female_4w_biological_rep3_vial_90412016202


title: rna-seq_spleen_training_female_4w_biological_rep4_vial_90416016202


title: rna-seq_spleen_training_male_4w_biological_rep5_vial_90292016202

source_name: RNA-Seq of Rat Male Spleen Powder Training - 4 weeks


title: rna-seq_spleen_training_female_4w_biological_rep2_vial_90410016202


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title: rna-seq_spleen_training_male_2w_biological_rep2_vial_90441016202


title: rna-seq_spleen_training_male_4w_biological_rep1_vial_90280016202


title: rna-seq_spleen_training_male_4w_biological_rep2_vial_90281016202


title: rna-seq_spleen_training_male_4w_biological_rep3_vial_90283016202


title: rna-seq_spleen_training_male_4w_biological_rep4_vial_90289016202


title: rna-seq_spleen_training_female_8w_biological_rep5_vial_90267016202

source_name: RNA-Seq of Rat Female Spleen Powder Training - 8 weeks


title: rna-seq_spleen_control_female_8w_biological_rep4_vial_90265016202

source_name: RNA-Seq of Rat Female Spleen Powder Control - 8 weeks


title: rna-seq_spleen_control_female_8w_biological_rep5_vial_90266016202


title: rna-seq_spleen_training_female_8w_biological_rep3_vial_90258016202


title: rna-seq_spleen_training_female_8w_biological_rep4_vial_90259016202


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source_name: RNA-Seq of Rat Male Spleen Powder Control - 8 weeks


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title: rna-seq_spleen_training_male_8w_biological_rep4_vial_90225016202

source_name: RNA-Seq of Rat Male Spleen Powder Training - 8 weeks


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source_name: RNA-Seq of Rat Female Colon Powder Training - 2 weeks

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source_name: RNA-Seq of Rat Female Colon Powder Training - 1 week


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source_name: RNA-Seq of Rat Male Colon Powder Training - 2 weeks


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source_name: RNA-Seq of Rat Male Colon Powder Training - 1 week


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source_name: RNA-Seq of Rat Female Colon Powder Training - 4 weeks

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source_name: RNA-Seq of Rat Male Colon Powder Training - 4 weeks


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source_name: RNA-Seq of Rat Female Colon Powder Training - 8 weeks


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source_name: RNA-Seq of Rat Female Colon Powder Control - 8 weeks


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source_name: RNA-Seq of Rat Male Colon Powder Training - 8 weeks


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source_name: RNA-Seq of Rat Male Adrenal Powder Training - 2 weeks


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source_name: RNA-Seq of Rat Male Adrenal Powder Training - 1 week


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source_name: RNA-Seq of Rat Male Adrenal Powder Training - 8 weeks


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source_name: RNA-Seq of Rat Male Heart Powder Training - 4 weeks


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source_name: RNA-Seq of Rat Female Heart Powder Training - 8 weeks


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source_name: RNA-Seq of Rat Male Heart Powder Control - 8 weeks


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source_name: RNA-Seq of Rat Female Vastus Lateralis Powder Training - 1 week


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source_name: RNA-Seq of Rat Male Vastus Lateralis Powder Training - 2 weeks


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source_name: RNA-Seq of Rat Male Vastus Lateralis Powder Training - 1 week


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source_name: RNA-Seq of Rat Female Vastus Lateralis Powder Training - 4 weeks


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source_name: RNA-Seq of Rat Male Vastus Lateralis Powder Training - 4 weeks


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source_name: RNA-Seq of Rat Female Vastus Lateralis Powder Training - 8 weeks


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source_name: RNA-Seq of Rat Female Vastus Lateralis Powder Control - 8 weeks


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source_name: RNA-Seq of Rat Male Vastus Lateralis Powder Control - 8 weeks


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source_name: RNA-Seq of Rat Female Gastrocnemius Powder Training - 1 week


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source_name: RNA-Seq of Rat Male Gastrocnemius Powder Training - 2 weeks


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source_name: RNA-Seq of Rat Female Gastrocnemius Powder Training - 4 weeks


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source_name: RNA-Seq of Rat Male Gastrocnemius Powder Training - 4 weeks


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source_name: RNA-Seq of Rat Female Gastrocnemius Powder Training - 8 weeks


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source_name: RNA-Seq of Rat Female Gastrocnemius Powder Control - 8 weeks


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source_name: RNA-Seq of Rat Female Hypothalamus Powder Training - 1 week


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source_name: RNA-Seq of Rat Male Hypothalamus Powder Training - 2 weeks


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source_name: RNA-Seq of Rat Male Hypothalamus Powder Training - 1 week


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source_name: RNA-Seq of Rat Female Hypothalamus Powder Training - 4 weeks


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source_name: RNA-Seq of Rat Male Hypothalamus Powder Training - 4 weeks


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source_name: RNA-Seq of Rat Female Hypothalamus Powder Control - 8 weeks


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source_name: RNA-Seq of Rat Male Hypothalamus Powder Training - 8 weeks


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source_name: RNA-Seq of Rat Female Cortex Powder Training - 4 weeks


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source_name: RNA-Seq of Rat Female Cortex Powder Control - 8 weeks


title: rna-seq_cortex_control_female_8w_biological_rep3_vial_90252015302


title: rna-seq_cortex_control_female_8w_biological_rep1_vial_90245015302


title: rna-seq_cortex_training_female_8w_biological_rep1_vial_90251015302


title: rna-seq_cortex_training_male_4w_biological_rep3_vial_90283015302


title: rna-seq_cortex_control_male_8w_biological_rep4_vial_90237015302

source_name: RNA-Seq of Rat Male Cortex Powder Control - 8 weeks


title: rna-seq_cortex_training_male_1w_biological_rep2_vial_90422015302


title: rna-seq_cortex_control_female_8w_biological_rep5_vial_90266015302


title: rna-seq_cortex_control_male_8w_biological_rep3_vial_90232015302


title: rna-seq_cortex_control_female_8w_biological_rep2_vial_90248015302


title: rna-seq_cortex_control_male_8w_biological_rep2_vial_90229015302


title: rna-seq_cortex_training_male_8w_biological_rep5_vial_90227015302

source_name: RNA-Seq of Rat Male Cortex Powder Training - 8 weeks


title: rna-seq_cortex_training_male_1w_biological_rep3_vial_90423015302


title: rna-seq_cortex_control_male_8w_biological_rep5_vial_90239015302


title: rna-seq_cortex_training_female_4w_biological_rep4_vial_90416015302


title: rna-seq_cortex_training_male_8w_biological_rep4_vial_90225015302


title: rna-seq_cortex_control_male_8w_biological_rep1_vial_90217015302


title: rna-seq_hippoc_training_female_2w_biological_rep4_vial_90585015202

description: motrpac_pass1b-06_t52-hippocampus_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Female Hippocampus Powder Training - 2 weeks

value: Hippocampus Powder


title: rna-seq_hippoc_training_female_2w_biological_rep5_vial_90587015202


title: rna-seq_cortex_training_male_8w_biological_rep3_vial_90223015302


title: rna-seq_hippoc_training_female_2w_biological_rep3_vial_90581015202


title: rna-seq_cortex_training_male_8w_biological_rep1_vial_90218015302


title: rna-seq_cortex_training_male_8w_biological_rep2_vial_90222015302


title: rna-seq_hippoc_training_female_2w_biological_rep2_vial_90578015202


title: rna-seq_hippoc_training_male_2w_biological_rep4_vial_90449015202

source_name: RNA-Seq of Rat Male Hippocampus Powder Training - 2 weeks


title: rna-seq_hippoc_training_female_1w_biological_rep2_vial_90560015202

source_name: RNA-Seq of Rat Female Hippocampus Powder Training - 1 week


title: rna-seq_hippoc_training_female_1w_biological_rep1_vial_90559015202


title: rna-seq_hippoc_training_female_2w_biological_rep1_vial_90576015202


title: rna-seq_hippoc_training_female_1w_biological_rep3_vial_90564015202


title: rna-seq_hippoc_training_female_1w_biological_rep4_vial_90567015202


title: rna-seq_hippoc_training_male_2w_biological_rep5_vial_90450015202


title: rna-seq_hippoc_training_male_2w_biological_rep3_vial_90444015202


title: rna-seq_hippoc_training_male_1w_biological_rep4_vial_90426015202

source_name: RNA-Seq of Rat Male Hippocampus Powder Training - 1 week


title: rna-seq_hippoc_training_male_1w_biological_rep3_vial_90423015202


title: rna-seq_hippoc_training_male_1w_biological_rep2_vial_90422015202


title: rna-seq_hippoc_training_male_1w_biological_rep1_vial_90421015202


title: rna-seq_hippoc_training_female_1w_biological_rep5_vial_90571015202


title: rna-seq_hippoc_training_male_2w_biological_rep2_vial_90441015202


title: rna-seq_hippoc_training_female_4w_biological_rep5_vial_90420015202

source_name: RNA-Seq of Rat Female Hippocampus Powder Training - 4 weeks


title: rna-seq_hippoc_training_female_4w_biological_rep2_vial_90410015202


title: rna-seq_hippoc_training_female_4w_biological_rep4_vial_90416015202


title: rna-seq_hippoc_training_male_1w_biological_rep5_vial_90430015202


title: rna-seq_hippoc_training_female_4w_biological_rep3_vial_90412015202


title: rna-seq_hippoc_training_male_4w_biological_rep5_vial_90292015202

source_name: RNA-Seq of Rat Male Hippocampus Powder Training - 4 weeks


title: rna-seq_hippoc_training_female_4w_biological_rep1_vial_90406015202


title: rna-seq_hippoc_training_male_4w_biological_rep4_vial_90289015202


title: rna-seq_hippoc_training_male_4w_biological_rep3_vial_90283015202


title: rna-seq_hippoc_training_male_4w_biological_rep1_vial_90280015202


title: rna-seq_hippoc_training_female_8w_biological_rep5_vial_90267015202

source_name: RNA-Seq of Rat Female Hippocampus Powder Training - 8 weeks


title: rna-seq_hippoc_training_female_8w_biological_rep4_vial_90259015202


title: rna-seq_hippoc_training_male_2w_biological_rep1_vial_90439015202


title: rna-seq_hippoc_training_female_8w_biological_rep3_vial_90258015202


title: rna-seq_hippoc_training_female_8w_biological_rep2_vial_90254015202


title: rna-seq_hippoc_control_female_8w_biological_rep1_vial_90245015202

source_name: RNA-Seq of Rat Female Hippocampus Powder Control - 8 weeks


title: rna-seq_hippoc_control_male_8w_biological_rep4_vial_90237015202

source_name: RNA-Seq of Rat Male Hippocampus Powder Control - 8 weeks


title: rna-seq_hippoc_control_male_8w_biological_rep5_vial_90239015202


title: rna-seq_hippoc_control_female_8w_biological_rep4_vial_90265015202


title: rna-seq_hippoc_control_female_8w_biological_rep2_vial_90248015202


title: rna-seq_hippoc_training_female_8w_biological_rep1_vial_90251015202


title: rna-seq_hippoc_control_male_8w_biological_rep3_vial_90232015202


title: rna-seq_hippoc_training_male_8w_biological_rep4_vial_90225015202

source_name: RNA-Seq of Rat Male Hippocampus Powder Training - 8 weeks


title: rna-seq_hippoc_training_male_8w_biological_rep5_vial_90227015202


title: rna-seq_hippoc_control_male_8w_biological_rep2_vial_90229015202


title: rna-seq_hippoc_control_female_8w_biological_rep3_vial_90252015202


title: rna-seq_hippoc_training_male_8w_biological_rep3_vial_90223015202


title: rna-seq_hippoc_training_male_8w_biological_rep2_vial_90222015202


title: rna-seq_blood_training_female_2w_biological_rep5_vial_90587013001

description: motrpac_pass1b-06_t30-blood-rna_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Female PaxGene RNA Training - 2 weeks

value: PaxGene RNA


title: rna-seq_hippoc_control_male_8w_biological_rep1_vial_90217015202


title: rna-seq_blood_training_female_2w_biological_rep3_vial_90581013001

value: Training - 2 weeks


title: rna-seq_hippoc_training_male_8w_biological_rep1_vial_90218015202


title: rna-seq_blood_training_female_2w_biological_rep4_vial_90585013001


title: rna-seq_hippoc_training_male_4w_biological_rep2_vial_90281015202


title: rna-seq_blood_training_female_2w_biological_rep2_vial_90578013001


title: rna-seq_blood_training_female_2w_biological_rep1_vial_90576013001


title: rna-seq_hippoc_control_female_8w_biological_rep5_vial_90266015202


title: rna-seq_blood_training_female_1w_biological_rep5_vial_90571013001

source_name: RNA-Seq of Rat Female PaxGene RNA Training - 1 week


title: rna-seq_blood_training_female_1w_biological_rep4_vial_90567013001


title: rna-seq_blood_training_female_1w_biological_rep3_vial_90564013001


title: rna-seq_blood_training_female_1w_biological_rep2_vial_90560013001


title: rna-seq_blood_training_female_1w_biological_rep1_vial_90559013001


title: rna-seq_blood_training_male_2w_biological_rep5_vial_90450013001

source_name: RNA-Seq of Rat Male PaxGene RNA Training - 2 weeks


title: rna-seq_blood_training_male_2w_biological_rep3_vial_90444013001


title: rna-seq_blood_training_male_2w_biological_rep2_vial_90441013002


title: rna-seq_blood_training_male_1w_biological_rep5_vial_90430013001

source_name: RNA-Seq of Rat Male PaxGene RNA Training - 1 week


title: rna-seq_blood_training_male_2w_biological_rep1_vial_90439013001


title: rna-seq_blood_training_male_1w_biological_rep4_vial_90426013001


title: rna-seq_blood_training_female_4w_biological_rep5_vial_90420013001

source_name: RNA-Seq of Rat Female PaxGene RNA Training - 4 weeks


title: rna-seq_blood_training_male_1w_biological_rep2_vial_90422013002


title: rna-seq_blood_training_male_1w_biological_rep1_vial_90421013002


title: rna-seq_blood_training_male_4w_biological_rep4_vial_90289013001

source_name: RNA-Seq of Rat Male PaxGene RNA Training - 4 weeks


title: rna-seq_blood_training_female_4w_biological_rep2_vial_90410013001


title: rna-seq_blood_training_male_4w_biological_rep1_vial_90280013001


title: rna-seq_blood_control_female_8w_biological_rep5_vial_90266013002

source_name: RNA-Seq of Rat Female PaxGene RNA Control - 8 weeks


title: rna-seq_blood_training_male_4w_biological_rep2_vial_90281013001


title: rna-seq_blood_training_female_8w_biological_rep5_vial_90267013002

source_name: RNA-Seq of Rat Female PaxGene RNA Training - 8 weeks


title: rna-seq_blood_control_female_8w_biological_rep4_vial_90265013001


title: rna-seq_blood_training_male_4w_biological_rep3_vial_90283013001


title: rna-seq_blood_training_female_8w_biological_rep4_vial_90259013002


title: rna-seq_blood_training_female_8w_biological_rep3_vial_90258013001


title: rna-seq_blood_training_female_8w_biological_rep2_vial_90254013002


title: rna-seq_blood_control_female_8w_biological_rep3_vial_90252013001


title: rna-seq_blood_control_female_8w_biological_rep2_vial_90248013001


title: rna-seq_blood_training_male_2w_biological_rep4_vial_90449013001


title: rna-seq_blood_training_male_1w_biological_rep3_vial_90423013002


title: rna-seq_blood_control_female_8w_biological_rep1_vial_90245013002


title: rna-seq_blood_control_male_8w_biological_rep5_vial_90239013002

source_name: RNA-Seq of Rat Male PaxGene RNA Control - 8 weeks


title: rna-seq_blood_training_female_4w_biological_rep4_vial_90416013001


title: rna-seq_blood_training_female_4w_biological_rep3_vial_90412013001


title: rna-seq_blood_training_female_4w_biological_rep1_vial_90406013001


title: rna-seq_blood_control_male_8w_biological_rep3_vial_90232013002


title: rna-seq_blood_training_male_4w_biological_rep5_vial_90292013001


title: rna-seq_blood_control_male_8w_biological_rep4_vial_90237013002


title: rna-seq_blood_training_male_8w_biological_rep3_vial_90223013002

source_name: RNA-Seq of Rat Male PaxGene RNA Training - 8 weeks


title: rna-seq_blood_training_male_8w_biological_rep1_vial_90218013001


title: rna-seq_blood_control_male_8w_biological_rep1_vial_90217013001


title: rna-seq_kidney_female_reference_5_vial_80029995909

description: motrpac_pass1b-06_t59-kidney_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Female Kidney Powder Reference

value: Kidney Powder

value: Reference


title: rna-seq_blood_training_female_8w_biological_rep1_vial_90251013001


title: rna-seq_kidney_male_reference_5_vial_80028885909

source_name: RNA-Seq of Rat Male Kidney Powder Reference


title: rna-seq_liver_female_reference_8_vial_80003996809

description: motrpac_pass1b-06_t68-liver_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Female Liver Powder Reference

value: Liver Powder


title: rna-seq_bat_female_reference_9_vial_80031996905

source_name: RNA-Seq of Rat Female Brown Adipose Powder Reference

value: Brown Adipose Powder


title: rna-seq_wat_female_reference_10_vial_80005997012

description: motrpac_pass1b-06_t70-white-adipose_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Female White Adipose Powder Reference

value: White Adipose Powder


title: rna-seq_wat_male_reference_10_vial_80004887012

source_name: RNA-Seq of Rat Male White Adipose Powder Reference


title: rna-seq_bat_male_reference_9_vial_80030886905

description: motrpac_pass1b-06_t69-brown-adipose_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Male Brown Adipose Powder Reference


title: rna-seq_liver_female_reference_8_vial_80003996808


title: rna-seq_liver_male_reference_8_vial_80002886808

source_name: RNA-Seq of Rat Male Liver Powder Reference


title: rna-seq_lung_female_reference_7_vial_80027996619

source_name: RNA-Seq of Rat Female Lung Powder Reference

value: Lung Powder


title: rna-seq_liver_male_reference_8_vial_80002886809


title: rna-seq_adrnl_female_reference_6_vial_80041996024

source_name: RNA-Seq of Rat Female Adrenal Powder Reference


title: rna-seq_heart_male_reference_4_vial_80032885819

description: motrpac_pass1b-06_t58-heart_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Male Heart Powder Reference

value: Heart Powder


title: rna-seq_adrnl_male_reference_6_vial_80040886026

source_name: RNA-Seq of Rat Male Adrenal Powder Reference


title: rna-seq_blood_control_male_8w_biological_rep2_vial_90229013002

value: Control - 8 weeks


title: rna-seq_blood_training_male_8w_biological_rep2_vial_90222013002

value: Training - 8 weeks


title: rna-seq_skm-gn_female_reference_3_vial_80001995533

source_name: RNA-Seq of Rat Female Gastrocnemius Powder Reference

value: Gastrocnemius Powder


title: rna-seq_blood_training_male_8w_biological_rep5_vial_90227013002


title: rna-seq_skm-gn_male_reference_3_vial_80000885532

source_name: RNA-Seq of Rat Male Gastrocnemius Powder Reference


title: rna-seq_blood_training_male_8w_biological_rep4_vial_90225013001


title: rna-seq_skm-gn_female_reference_3_vial_80001995542


title: rna-seq_skm-gn_female_reference_3_vial_80001995532


title: rna-seq_skm-gn_female_reference_3_vial_80001995540


title: rna-seq_skm-gn_female_reference_3_vial_80001995528


title: rna-seq_hippoc_female_reference_2_vial_80035995205

source_name: RNA-Seq of Rat Female Hippocampus Powder Reference


title: rna-seq_hippoc_female_reference_2_vial_80035995207


title: rna-seq_hippoc_female_reference_2_vial_80035995206


title: rna-seq_hippoc_male_reference_2_vial_80034885205

source_name: RNA-Seq of Rat Male Hippocampus Powder Reference


title: rna-seq_skm-gn_male_reference_3_vial_80000885510


title: rna-seq_blood_female_reference_1_vial_80007993006

source_name: RNA-Seq of Rat Female PaxGene RNA Reference


title: rna-seq_hippoc_male_reference_2_vial_80034885206


title: rna-seq_lung_male_reference_7_vial_80026886619

description: motrpac_pass1b-06_t66-lung_transcript-rna-seq_rsem-genes-count.txt

source_name: RNA-Seq of Rat Male Lung Powder Reference


title: Male4

city: Fort Worth

first: J.

middle: Thomas

last: Cunningham

state: TX

address: 3500 Camp Bowie Blvd

department: Physiology & Anatomy

institute: UNT Health Science Center

description: Fresh frozen spatial transcriptome sequencing

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger pipelines
Data were analyzed using Loup Browser (v 6.0.0, 10x Genomics) and one supraoptic nucleus per section was identified. The corresponding barcoded spots were further analyzed using Loupe Browser Significant Feature Comparison, globally distinguishing option. The data were analyzed with transcripts with low average counts included.
The data from the selected barcoded spots overlaying the supraoptic nucleus in each sample were extracted and eported using Seurat and custom srcipts, which were used for subsequent analyses (e.g., DEseq2 and RUVSeq analyses).
Heatmaps were created using pheatmap in R (https://www.rdocumentation.org/packages/pheatmap/versions/1.0.12/topics/pheatmap).
Gene Ontology analyses were performed using ShinyGO 0.77 and other bioinformatic tools at http://geneontology.org/. Data were also analyzed with QIAGEN Ingenuity Pathway Analysis (IPA) (QIAGEN Inc., https://digitalinsights.qiagen.com/IPA.
Assembly: mRatBN7.2

molecule: polyA RNA

source_name: Male brain section containing the medial hypothalamus

extract_protocol:
Ten micron frozen sections were placed inside the capture area of a Visium Spatial Gene Expression slide (PN-2000233, 10x Genomics). The sections were fixed, stained for H&E and imaged using a Keyence BZ-X810 microscope according to 10x Genomics protocol CG000160. After the tissue was permeabilized according to the manufacturer’s instructions, libraries were prepared and constructed according to the Visium Spatial Gene Expression User Guide (CG000239, 10x Genomics). Sequencing was performed using the NovaSeq 6000 System (Illumnia, Inc., San Diego, CA, USA) at a minimum sequencing depth of 50,000 read pairs per barcode region using the following read code protocol: read 1 – 28 cycles, i7 index – 10 cycles, i5 index – 10 cycles, and read 2 – 90 cycles.
The libraries were prepared and constructed using the Visium Spatial Gene Expression User Guide (CG000239, 10x Genomics).
Other: Spatial Transcriptomics

treatment_protocol: The rats were housed individually under standard laboratory conditions with a 12:12 light:dark cycle and ad libidum food and water. They anesthetized with isoflurane at the time of sacrifice (2% in 95% O2).

tag: genotype

value: Sprague Dawley


title: Male3

value: Male brain section containing the medial hypothalamus


title: Male2


title: rna-seq_heart_female_reference_4_vial_80033995819

source_name: RNA-Seq of Rat Female Heart Powder Reference


title: Male1


title: rna-seq_skm-gn_male_reference_3_vial_80000885540


title: rna-seq_skm-gn_female_reference_3_vial_80001995510


title: rna-seq_skm-gn_male_reference_3_vial_80000885537


title: rna-seq_skm-gn_male_reference_3_vial_80000885541


title: Female4

source_name: Female brain section containing the medial hypothalamus


title: rna-seq_skm-gn_male_reference_3_vial_80000885533


title: Female2

value: Female brain section containing the medial hypothalamus


title: rna-seq_hippoc_male_reference_2_vial_80034885207


title: Female3


title: Female1


title: rna-seq_blood_male_reference_1_vial_80006883006

source_name: RNA-Seq of Rat Male PaxGene RNA Reference