title: LT_A_ctrl, Animal B19, Frontal_cortex

description:
RNAseq batch3
B19_FCTX


title: Whole Blood Transcriptome Baseline D23V1

status: Public on Nov 20 2025

type: SRA

city: Boston

first: Adriana

last: Tomic

address: 650 Albany St.

country: USA

institute: Boston University

description: Library name: D23V1

library_source: transcriptomic

data_processing:
Raw sequencing reads were quality controlled and then aligned and quantified using Salmon (v1.x) against the human reference transcriptome (hg38). Transcript-level counts were aggregated to gene-level counts for analysis.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Comma-separated values (CSV) matrix containing gene-level counts. Rows represent genes and columns represent samples. Counts were aggregated from transcript-level abundance estimates generated by Salmon.

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Total RNA was extracted from Paxgene-stabilized whole blood using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Sequencing libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina) to preserve strand information and deplete ribosomal RNA.

treatment_protocol: Samples were collected at Visit 1 (Baseline) immediately prior to vaccination.

tag: tissue

value: whole blood

tag: age

tag: Sex

value: female

tag: group

tag: treatment

value: Baseline (Pre-vaccination)


title: A54_Adipose

type: genomic

city: Hong Kong

first: Andrew

middle: J.

last: Kwok

address: 30-32 Ngan Shing Street, Shatin, New Territories

department: Medicine and Therapeutics

country: Hong Kong

institute: Chinese University of Hong Kong

description:
A54
208114950077_R05C01

hyb_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array

data_processing:
Raw data were processed with SeSaMe (v1.16.1)
Processed data are presented in the form of beta values.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Mus musculus

source_name: Adipose

extract_protocol: Genomic DNA was extracted with the Quick-DNA Miniprep Plus Kit (D4069, Zymo Research) for blood or EZNA Tissue DNA Kit (D3396-02, Omega Bio-Tek) for solid tissue)

value: Adipose


title: Whole Blood Transcriptome Baseline D17V1

description: Library name: D17V1


title: Whole Blood Transcriptome Baseline D16V1

description: Library name: D16V1

value: male


title: Whole Blood Transcriptome Baseline D14V1

description: Library name: D14V1


title: LT_A_ctrl, Animal B16, Skeletal_muscle

description:
RNAseq batch3
B16_SkeletalMuscle

data_processing:
Raw sequencing FASTQ files were mapped with STAR98 (v2.7.10b) with default parameters using the Mus musculus genome assembly GRCm39.
Quality control was carried out with the FastQC (v0.11.9) and MultiQC99 (v1.13a) packages.
HTSeq100 (v2.0.2) was used to obtain read counts with default options except ‘mode’ being set to ‘intersection-strict’, and ‘nonunique’ being set to ‘fraction’ for ambiguous reads. Gene counts were filtered for a minimum of at least 10 reads in a minimum number of samples, with the minimum number based on the number of animals constituting the smallest comparator group size in the experiment.
Assembly: GRCm39
Supplementary files format and content: CSV file with raw counts
Supplementary files format and content: CSV metadata file

molecule: polyA RNA

extract_protocol:
The tissues were retrieved from RNAlater (AM7021, Thermo Fisher Scientific, US), combined with the TRIzol reagent (15596018, Thermo Fisher Scientific, US) or the lysis buffer of the RNAqueous kit (AM1912, Thermo Fisher Scientific, US), homogenized using the TissueLyser II system (Qiagen, US), and total RNA extraction was performed following the instructions in the vendor’s manuals.
Total RNA samples were sent for library preparation and sequencing by Novogene (Novogene Biology Information Technology Co., Ltd., Beijing, China). Libraries were prepared with a poly(A) selection strategy using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770, New England Biolabs, US).


title: LT_A_ctrl, Animal B19, Adipose_tissue

description:
RNAseq batch3
B19_Adipose


title: A58_FCTX

description:
A58
208114950077_R04C01

scan_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array

source_name: FCTX

value: FCTX


title: Whole Blood Transcriptome Baseline D9V1

description: Library name: D9V1


title: Whole Blood Transcriptome Baseline D3V1

description: Library name: D3V1


title: Whole Blood Transcriptome Baseline D10V1

description: Library name: D10V1


title: LT_A_ctrl, Animal B16, Spleen

description:
RNAseq batch3
B16_Spleen

source_name: Spleen

value: Spleen


title: A54_FCTX

description:
A54
208114950077_R03C01

label_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array


title: Whole Blood Transcriptome Baseline D6V1

description: Library name: D6V1


title: Whole Blood Transcriptome Baseline D5V1

description: Library name: D5V1


title: Whole Blood Transcriptome Baseline D1V1

description: Library name: D1V1


title: LT_A_ctrl, Animal B16, Lung

description:
RNAseq batch3
B16_Lung

source_name: Lung

value: Lung


title: A58_Hippo

description:
A58
208114950077_R02C01

source_name: Hippo

value: Hippo


title: LT_A_ctrl, Animal B16, Liver

description:
RNAseq batch3
B16_Liver

source_name: Liver

value: Liver


title: Nef6 heart

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

country: China

institute: Fujian University of Traditional Chinese Medicine

description: SHR  with 10-week neferine (10mg/kg/d) treatment

data_processing:
Data were filtered using the following specifications fastq software. The filtering standards from raw data to clean reads are: check the sample for contamination and, if there is pollution, remove it if the reads contains a joint sequence, the joint sequence is cut off first a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window, remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed, if the truncated read length is less than 50 bp, the entire read is removedRemove unmatched reads Q30，Q20 explanation： Q30 indicates that the sequencing error rate of the base is 0.1%. Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each sample

organism: Rattus norvegicus

source_name: heart tissue

extract_protocol:
The heart tissues were dissected and  stored in RNA later.Total RNA was extracted with  TRIzol® Reagent (Invitrogen,Carlsbad, CA, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer's instructions.

treatment_protocol: The SHRs were randomly divided into 2 groups: SHR, and SHR + neferine (10mg/kg/d) groups. WKY rats were set as control. Rats in WKY and SHR groups were  intragastrically with double distilled water (dd H2O), while rats in  SHR + neferine (10mg/kg/d) group were intragastrically with 10 mg/kg/d of neferine for 10 weeks.

tag: strain

value: SHR

value: heart tissue

tag: genotype

value: double distilled water

value: neferine

value: SHR+nefrine


title: Nef4 heart


title: Nef3 heart


title: LT_A_ctrl, Animal B16, Hippocampus

description:
RNAseq batch3
B16_Hipp

source_name: Hippocampus

value: Hippocampus


title: B25_Colon

description:
B25
208114950075_R05C02

source_name: Colon

value: Colon


title: LT_A_ctrl, Animal B16, Heart

description:
RNAseq batch3
B16_Heart

source_name: Heart

value: Heart


title: LT_A_ctrl, Animal B16, Kidney

description:
RNAseq batch3
B16_Kid

source_name: Kidney

value: Kidney


title: SHR4 heart

description: SHR  with 10-week  double distilled water  treatment


title: SHR3 heart


title: Nef5 heart


title: Nef1 heart


title: B36_Colon

description:
B36
208114950075_R06C02


title: Nef2 heart


title: SHR6 heart


title: B36_Adipose

description:
B36
208114950075_R04C02


title: B25_Adipose

description:
B25
208114950075_R03C02


title: LT_A_ctrl, Animal B16, Hypothalamus

description:
RNAseq batch3
B16_HTH

source_name: Hypothalamus

value: Hypothalamus


title: SHR1 heart

description: WKY with 10-week double distilled water treatment


title: WKY6 heart

value: WKY


title: B36_FCTX

description:
B36
208114950075_R02C02


title: WKY5 heart


title: WKY4 heart


title: A54_Hippo

description:
A54
208114950077_R01C01


title: B25_FCTX

description:
B25
208114950075_R01C02


title: LT_A_ctrl, Animal B16, Adipose_tissue

description:
RNAseq batch3
B16_Adipose


title: WKY3 heart


title: B36_Hippo

description:
B36
208114950075_R06C01


title: albas_rep2

city: Shanghai

first: Haoran

last: Ge

address: Songhu Road 2005

institute: Fudan university

description: Library name: albah_rep2

data_processing:
For lariat RNA-seq, raw reads was filtered by using Fastp (v0.23.2) to remove adapter and low-quality reads with parameters “-z 4 -q 20 -n 10 -c -t 1”. Alignment was performed with the HISAT2 (v2.2.1) using TAIR10 reference genome from Ensembl Plants with default parameters, and duplicates were removed by Samtools markdup (v1.14). Subread featureCounts was used to obtain counts for intron and loop region with parameters “-p -C -O -M - -fraction - -fracOverlap 1”, tail region with parameters “-p -C -O -M - -fraction - -minOverlap 10”. To normalize expression, FPKM of loop region was calculated with custom R script, and those transcripts with FPKM≥5 and the ratio of loop/tail ((loop reads/loop length)/(tail reads/tail length))>2 in all three replicates were identified as lariat RNAs.
The RIP-seq libraries were aligned to the genome with hisat2. BAM ﬁles with R1 reads were generated using SAMtools. The BAM files were used as input of MACS2 (input as control) for peak calling.
For lncRNA-seq analysis, raw reads was processed as the similar pipeline with lariat RNA-seq. FPKM of parent genes was calculated by StringTie (v2.2.1) with parameters “-e -G” .
Assembly: Ensembl
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
For lariat RNA-seq, total RNA of 0.5 g seedlings under normal condition and cold treatment was isolated using TRIzol (Ambion). For RIP-seq,  samples (~2 g) were fast-frozen and ground to fine powder in liquid N2. The resulting fine powder was suspended in 4 ml lysis buffer (50 mM Tris-HCl-Cl pH 8.0, 200 mM NaCl, 5 mM MgCl2, 10% Glycerol, 0.2% NP-40, 1 mM DTT, 1x protease inhibitor cocktail, 1 mM PMSF, 50 μM MG132 and 1 U/µl RNase inhibitor) at 4℃ for 30 min. Then the supernatant was passed through two layers of Miracloth. After centrifuged 3 times at 15,000 g for 10 min per time at 4℃, 100 µl of each sample was saved as input. The remaining supernatant was incubated with 50 μl of lysis buffer prewashed GFP-Trap agarose beads (Chromotek, gta-20) for 3 h at 4℃. Following IP, the beads were washed two times with lysis buffer, two times with low-salt wash buffer (200 mM LiCl, 0.1% SDS, 1% NP-40) and two times with high-salt wash buffer (500 mM NaCl, 0.1% SDS, 1% NP-40). To dissociate the RNA from the protein, the beads with buffer were added equal volume RNA elution buffer (100 mM Tris-HCl (pH 8.0), 400 mM NaCl, 2% SDS and 20 mM EDTA) and 20 mg/ml Proteinase K (Thermo, EO0491) and incubated at 65°C for 2 h with rotation. RNA was isolated with Trizol reagent. To detect more intron binding sites of these proteins, the input RNA and IPed RNA were incubated with RNase R (Epicentre, RNR07250) at 37°C for 1 h. Then, RNA was purified using the RNA Clean & Concentrator-5 (Zymo Research, R1016) following the manufacturer’s instructions and eluted in 10 μl nuclease-free water.
Total RNA and RIPed were firstly digested by RQ1 Dnase(Promega). RNA after RNase R digetion was purified using the RNA Clean & Concentrator-5 (Zymo Research) following the manufacturer’s instructions. A Ribo-off kit (Vazyme, Nanjing, China) was used to remove rRNA from the above RNase Rtreated RNA. 50 ng of RNA for each sample was fragmented with Frag/Prime Buffer (Vazyme) at 80°C for 1 min and used as the starting material for strand-specific RNA-seq library preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme).

value: seedling

value: albas


title: albas_rep1

description: Library name: albah_rep1


title: B25_Hippo

description:
B25
208114950075_R05C01


title: LT_A_ctrl, Animal B39, Liver

description:
RNAseq batch3
B39_Liver


title: albas_rep3

description: Library name: albah_rep3


title: SHR2 heart


title: B24_Colon

description:
B24
208114950075_R03C01


title: LT_A_ctrl, Animal B16, Frontal_cortex

description:
RNAseq batch3
B16_FCTX


title: LT_A_Ex, Animal B28, Liver

description:
RNAseq batch3
B28_Liver


title: B39_Adipose

description:
B39
208114950075_R02C01

value: Adipose


title: LT_A_Ex, Animal B26, Liver

description:
RNAseq batch3
B26_Liver


title: IP_ALBA5-GFP_dbr1-2_rep1

description: Library name: IP_ALBA5-GFP_dbr1-2_rep1


title: B39_Colon

description:
B39
208114950075_R04C01


title: IP_GFP_dbr1-2_rep2

description: Library name: IP_GFP_dbr1-2_rep2


title: LT_A_Ex, Animal B25, Liver

description:
RNAseq batch3
B25_Liver


title: input_GFP_dbr1-2_rep2

description: Library name: input_GFP_dbr1-2_rep2


title: IP_GFP_dbr1-2_rep1

description: Library name: IP_GFP_dbr1-2_rep1


title: IP_ALBA5-GFP_dbr1-2_rep2

description: Library name: IP_ALBA5-GFP_dbr1-2_rep2


title: LT_A_ctrl, Animal B16, Colon

description:
RNAseq batch3
B16_Colon


title: input_ALBA5-GFP_dbr1-2_rep1

description: Library name: input_ALBA5-GFP_dbr1-2_rep1


title: B24_Adipose

description:
B24
208114950075_R01C01


title: WKY1 heart


title: input_GFP_dbr1-2_rep1

description: Library name: input_GFP_dbr1-2_rep1


title: LT_A_ctrl, Animal B24, Liver

description:
RNAseq batch3
B24_Liver


title: input_ALBA5-GFP_dbr1-2_rep2

description: Library name: input_ALBA5-GFP_dbr1-2_rep2


title: B39_FCTX

description:
B39
208114950072_R06C02

value: FCTX


title: FT_REF6ΔZnF#1_H3K27me3_ZT4_rep2

city: Xianyang

first: Jingyun

last: Lu

state: Shanxi

address: No. 22, Xinong Road

institute: Northwest A&F University

description: Library name: FT_REF6ΔZnF#1_H3K27me3_ZT4_rep2

library_source: genomic

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1. Reads were mapped to the Arabidopsis (TAIR10) genome with Botiew2 version 2.4.2.
Duplicate reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
For data visualization, data from two biological replicates were merged, and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp.
Average ChIP-seq profiles were generated using deepTools utility plotProfile.
Assembly: TAIR10
Supplementary files format and content: bigwig

source_name: Seedlings

growth_protocol: Plants were grown under long day conditions (16h light/8h dark) at 22°C

extract_protocol:
Chromatin was resuspended with ChIP lysis buffer and sheared to generate 200 bp-500 bp fragments.Sheared chromatin was diluted four times with ChIP dilution buffer.Immunoprecipitation was conducted with anti-H3K27me3 (Millipore, 07-449).
The immunoprecipitated DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction.

treatment_protocol: ChIP-seq was performed using 10-day-old seedlings at ZT4h, which were fixed with 1% formaldehyde.

value: Seedlings


title: LT_A_ctrl, Animal B27, Liver

description:
RNAseq batch3
B27_Liver

value: Liver


title: FT_REF6ΔZnF#1_H3K27me3_ZT4_rep1

description: Library name: FT_REF6ΔZnF#1_H3K27me3_ZT4_rep1


title: B24_FCTX

description:
B24
208114950072_R05C02


title: LT_A_ctrl, Animal B15, Liver

description:
RNAseq batch3
B15_Liver


title: Col_H3K27me3_ZT4_rep1

description: Library name: Col_H3K27me3_ZT4_rep1


title: LT_A_Ex, Animal B13, Liver

description:
RNAseq batch3
B14_Liver


title: Col_H3K27me3_ZT4_rep2

description: Library name: Col_H3K27me3_ZT4_rep2


title: ALBA5-GFP_alba456_rep3

description: Library name: LariatRNA_ALBA5-GFP_alba456_rep3

data_processing:
For lariat RNA-seq, raw reads was filtered by using Fastp (v0.23.2) to remove adapter and low-quality reads with parameters “-z 4 -q 20 -n 10 -c -t 1”. Alignment was performed with the HISAT2 (v2.2.1) using TAIR10 reference genome from Ensembl Plants with default parameters, and duplicates were removed by Samtools markdup (v1.14). Subread featureCounts was used to obtain counts for intron and loop region with parameters “-p -C -O -M - -fraction - -fracOverlap 1”, tail region with parameters “-p -C -O -M - -fraction - -minOverlap 10”. To normalize expression, FPKM of loop region was calculated with custom R script, and those transcripts with FPKM≥5 and the ratio of loop/tail ((loop reads/loop length)/(tail reads/tail length))>2 in all three replicates were identified as lariat RNAs.
The RIP-seq libraries were aligned to the genome with BWA. BAM ﬁles with R1 reads were generated using SAMtools. The BAM files were used as input of MACS2 (input as control) for peak calling.
Assembly: Ensembl
Supplementary files format and content: bigWig

treatment_protocol: For cold treatment, 2-week-old seedlings growing under 22 ℃ were transferred into 4 ℃ for another 3 hours or 24 hours cultivation.


title: B39_Hippo

description:
B39
208114950072_R04C02

value: Hippo


title: ALBA5-GFP_alba456_rep2

description: Library name: LariatRNA_ALBA5-GFP_alba456_rep2


title: ALBA5-GFP_alba456_rep1

description: Library name: LariatRNA_ALBA5-GFP_alba456_rep1


title: LT_A_Ex, Animal B14, Liver

description:
RNAseq batch3
B13_Liver


title: LT_Y_ctrl, Animal A58, Liver

description:
RNAseq batch3
A58_Liver


title: A53_Colon

description:
A53
208114950072_R01C02


title: LT_Y_ctrl, Animal A57, Liver

description:
RNAseq batch3
A57_Liver


title: B24_Hippo

description:
B24
208114950072_R03C02


title: dbr1_alba456_4_24h_rep3

description: Library name: LariatRNA_dbr1_alba456_4_24h_rep3

value: dbr1-2 alba456


title: dbr1_alba456_4_24h_rep2

description: Library name: LariatRNA_dbr1_alba456_4_24h_rep2


title: ALBA5_KE-GFP_alba456_rep3

description: Library name: LariatRNA_ALBA5_KE-GFP_alba456_rep3


title: ALBA5_KE-GFP_alba456_rep1

description: Library name: LariatRNA_ALBA5_KE-GFP_alba456_rep1


title: LT_Y_ctrl, Animal A55, Liver

description:
RNAseq batch3
A55_Liver


title: ALBA5_KE-GFP_alba456_rep2

description: Library name: LariatRNA_ALBA5_KE-GFP_alba456_rep2


title: A57_Adipose

description:
A57
208114950072_R06C01


title: dbr1_alba456_4_24h_rep1

description: Library name: LariatRNA_dbr1_alba456_4_24h_rep1


title: alba456_4_24h_rep2

description: Library name: LariatRNA_alba456_4_24h_rep2


title: A53_Adipose

description:
A53
208114950072_R05C01


title: alba456_4_24h_rep1

description: Library name: LariatRNA_alba456_4_24h_rep1


title: LT_A_ctrl, Animal B34, Liver

description:
RNAseq batch3
B34_Liver


title: A57_FCTX

description:
A57
208114950072_R04C01


title: dbr1_4_24h_rep3

description: Library name: LariatRNA_dbr1_4_24h_rep3


title: A57_Colon

description:
A57
208114950072_R02C02


title: A53_FCTX

description:
A53
208114950072_R03C01


title: LT_Y_ctrl, Animal A54, Skeletal_muscle

description:
RNAseq batch3
A54_SkeletalMuscle


title: dbr1_4_24h_rep2

description: Library name: LariatRNA_dbr1_4_24h_rep2


title: LT_Y_ctrl, Animal A56, Liver

description:
RNAseq batch3
A56_Liver


title: dbr1_4_24h_rep1

description: Library name: LariatRNA_dbr1_4_24h_rep1


title: LT_Y_ctrl, Animal A54, Spleen

description:
RNAseq batch3
A54_Spleen

value: Spleen


title: alba456_4_24h_rep3

description: Library name: LariatRNA_alba456_4_24h_rep3


title: LT_Y_ctrl, Animal A54, Lung

description:
RNAseq batch3
A54_Lung

value: Lung


title: A53_Hippo

description:
A53
208114950072_R01C01


title: Col-0_4_24h_rep2

description: Library name: LariatRNA_Col-0_4_24h_rep2

value: WT


title: A57_Hippo

description:
A57
208114950072_R02C01


title: DBR1_H85A-GFP-IP_wt_rep2

description: Library name: DBR1_H85A-GFP-IP_wt_rep2

library_source: other

molecule: other


title: LT_Y_ctrl, Animal A54, Liver

description:
RNAseq batch3
A54_Liver


title: DBR1_H85A-GFP-IP_alba456_rep2

description: Library name: DBR1_H85A-GFP-IP_alba456_rep2


title: DBR1_H85A-GFP-IP_wt_rep1

description: Library name: DBR1_H85A-GFP-IP_wt_rep1


title: LT_Y_ctrl, Animal A54, Kidney

description:
RNAseq batch3
A54_Kid


title: Col-0_4_24h_rep1

description: Library name: LariatRNA_Col-0_4_24h_rep1


title: B14_Colon

description:
B14
208114950065_R05C02


title: ALBA5-GFP-IP_wt_rep2

description: Library name: ALBA5-GFP-IP_wt_rep2


title: ALBA5-GFP-IP_wt_rep1

description: Library name: ALBA5-GFP-IP_wt_rep1


title: GFP-IP_rep2

description: Library name: GFP-IP_rep2


title: B30_Colon

description:
B30
208114950065_R06C02


title: LT_Y_ctrl, Animal A54, Hippocampus

description:
RNAseq batch3
A54_Hipp

value: Hippocampus


title: B30_Adipose

description:
B30
208114950065_R04C02


title: GFP-IP_rep1

description: Library name: GFP-IP_rep1


title: Col-0_4_24h_rep3

description: Library name: LariatRNA_Col-0_4_24h_rep3


title: LT_Y_ctrl, Animal A54, Heart

description:
RNAseq batch3
A54_Heart


title: input_DBR1_H85A-GFP-IP_alba456_rep2

description: Library name: input_DBR1_H85A-GFP-IP_alba456_rep2


title: B14_Adipose

description:
B14
208114950065_R03C02


title: LT_Y_ctrl, Animal A54, Hypothalamus

description:
RNAseq batch3
A54_HTH


title: B30_FCTX

description:
B30
208114950065_R02C02


title: input_DBR1_H85A-GFP-IP_wt_rep2

description: Library name: input_DBR1_H85A-GFP-IP_wt_rep2


title: input_DBR1_H85A-GFP-IP_alba456_rep1

description: Library name: input_DBR1_H85A-GFP-IP_alba456_rep1


title: LT_Y_ctrl, Animal A54, Colon

description:
RNAseq batch3
A54_Colon

value: Colon


title: DBR1_H85A-GFP-IP_alba456_rep1

description: Library name: DBR1_H85A-GFP-IP_alba456_rep1


title: input_DBR1_H85A-GFP-IP_wt_rep1

description: Library name: input_DBR1_H85A-GFP-IP_wt_rep1


title: input_ALBA5-GFP-IP_wt_rep2

description: Library name: input_ALBA5-GFP-IP_wt_rep2


title: B14_FCTX

description:
B14
208114950065_R01C02


title: B30_Hippo

description:
B30
208114950065_R06C01


title: LT_Y_ctrl, Animal A54, Adipose_tissue

description:
RNAseq batch3
A54_Adipose


title: input_GFP-IP_rep2

description: Library name: input_GFP-IP_rep2


title: input_GFP-IP_rep1

description: Library name: input_GFP-IP_rep1


title: dbr1_alba456_rep2

description: Library name: LariatRNA_dbr1_alba456_rep2


title: dbr1_alba456_rep3

description: Library name: LariatRNA_dbr1_alba456_rep3


title: B37_Colon

description:
B37
208114950065_R04C01


title: LT_Y_ctrl, Animal A53, Lung

description:
RNAseq batch3
A53_Lung


title: LT_Y_ctrl, Animal A53, Spleen

description:
RNAseq batch3
A53_Spleen


title: alba456_rep3

description: Library name: LariatRNA_alba456_rep3


title: dbr1_alba456_rep1

description: Library name: LariatRNA_dbr1_alba456_rep1


title: alba456_rep2

description: Library name: LariatRNA_alba456_rep2


title: B19_Colon

description:
B19
208114950065_R03C01


title: LT_Y_ctrl, Animal A53, Liver

description:
RNAseq batch3
A53_Liver


title: alba456_rep1

description: Library name: LariatRNA_alba456_rep1


title: dbr1_rep3

description: Library name: LariatRNA_dbr1_rep3


title: B37_Adipose

description:
B37
208114950065_R02C01


title: B19_Adipose

description:
B19
208114950065_R01C01


title: dbr1_rep1

description: Library name: LariatRNA_dbr1_rep1


title: dbr1_rep2

description: Library name: LariatRNA_dbr1_rep2


title: input_ALBA5-GFP-IP_wt_rep1

description: Library name: input_ALBA5-GFP-IP_wt_rep1


title: Col-0_rep3

description: Library name: LariatRNA_Col-0_rep3


title: LT_Y_ctrl, Animal A54, Frontal_cortex

description:
RNAseq batch3
A54_FCTX


title: B14_Hippo

description:
B14
208114950065_R05C01


title: Col-0_rep2

description: Library name: LariatRNA_Col-0_rep2


title: LT_Y_ctrl, Animal A53, Hippocampus

description:
RNAseq batch3
A53_Hipp


title: B19_FCTX

description:
B19
208114950057_R05C02


title: B37_FCTX

description:
B37
208114950057_R06C02


title: Col-0_rep1

description: Library name: LariatRNA_Col-0_rep1


title: LT_Y_ctrl, Animal A53, Heart

description:
RNAseq batch3
A53_Heart

value: Heart


title: LT_Y_ctrl, Animal A53, Hypothalamus

description:
RNAseq batch3
A53_HTH


title: B37_Hippo

description:
B37
208114950057_R04C02


title: LT_Y_ctrl, Animal A53, Colon

description:
RNAseq batch3
A53_Colon


title: LT_Y_ctrl, Animal A53, Frontal_cortex

description:
RNAseq batch3
A53_FCTX


title: A56_Colon

description:
A56
208114950057_R02C02


title: LT_Y_ctrl, Animal A53, Kidney

description:
RNAseq batch3
A53_Kid

value: Kidney


title: B19_Hippo

description:
B19
208114950057_R03C02


title: LT_Y_ctrl, Animal A53, Adipose_tissue

description:
RNAseq batch3
A53_Adipose


title: H216_DNA_wk36

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

data_processing:
Raw reads were trimmed for low quality reads and miscalled nucleotides using Trimmomatic v. 0.36.
Reads that passed the trimming step were aligned to rhesus macaque genome (Ensembl Mmul_8.0.1 release 88) using the STAR aligner (version 2.5.3a).
Aligned reads were counted using HTSeq (version 0.9.1).
Genome_build: Ensembl Mmul_8.0.1 release 88.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
RNA was extracted from PAXgene samples using the PAXgene Blood RNA kit (PreAnalytiX) according to the manufacturer’s instructions.
GLOBINclear kit (Ambion, Austin, TX, USA) was used to remove globin transcript. Libraries were loaded on Illumina Truseq Paired-End stranded mRNA Kits and sequenced in 2 x 51 base paired-end runs on an Illumina HiSeq 2500 sequencer with an average of 20 million reads per sample.

tag: animal id

tag: gender

value: F

tag: nb. of challenges to infection

value: DNA group

tag: timepoint

tag: batch

tag: vaccine

value: DNA


title: H163_DNA_wk12


title: DEGI_DNA_pre

value: DEGI

value: M

value: Pre Vacc


title: 045_ALVAC_pre

value: ALVAC group

value: ALVAC


title: M61_ALVAC_wk36


title: A52_Colon

description:
A52
208114950057_R01C02


title: M36_DNA_pre


title: 036_DNA_wk36


title: LT_Y_ctrl, Animal A52, Liver

description:
RNAseq batch3
A52_Liver

value: Liver


title: A56_Adipose

description:
A56
208114950057_R06C01

value: Adipose


title: M88_DNA_pre


title: H163_DNA_wk36


title: DETE_ALVAC_wk36

value: DETE


title: LT_Y_ctrl, Animal A51, Spleen

description:
RNAseq batch3
A51_Spleen

value: Spleen


title: MRD_ALVAC_wk12

value: MRD


title: LT_Y_ctrl, Animal A51, Lung

description:
RNAseq batch3
A51_Lung

value: Lung


title: 01F_ALVAC_wk36


title: DFAN_DNA_pre

value: DFAN


title: M88_DNA_wk36


title: A56_FCTX

description:
A56
208114950057_R04C01

value: FCTX


title: LT_Y_ctrl, Animal A51, Liver

description:
RNAseq batch3
A51_Liver


title: DFGF_DNA_wk12

value: DFGF


title: A52_FCTX

description:
A52
208114950057_R03C01


title: DFRF_DNA.control_wk12

value: DFRF

value: Controls challenged with DNA group

value: DNA control


title: H304_ALVAC_pre

value: F


title: DFNF_ALVAC_pre

value: DFNF

value: M


title: A56_Hippo

description:
A56
208114950057_R02C01

value: Hippo


title: DFGL_ALVAC_wk36

value: DFGL

value: ALVAC group

value: ALVAC


title: LT_Y_ctrl, Animal A51, Heart

description:
RNAseq batch3
A51_Heart

value: Heart


title: DFAW_ALVAC_pre

value: DFAW

value: Pre Vacc


title: A52_Hippo

description:
A52
208114950057_R01C01


title: DFNB_ALVAC.control_pre

value: DFNB

value: Controls challenged with ALVAC group

value: ALVAC control


title: B13_Colon

description:
B13
208114950054_R05C02

value: Colon


title: B28_Colon

description:
B28
208114950054_R06C02


title: LT_Y_ctrl, Animal A51, Hippocampus

description:
RNAseq batch3
A51_Hipp

value: Hippocampus


title: DFGZ_ALVAC.control_wk36

value: DFGZ


title: A52_Adipose

description:
A52
208114950057_R05C01

value: Adipose


title: LT_Y_ctrl, Animal A51, Hypothalamus

description:
RNAseq batch3
A51_HTH

value: Hypothalamus


title: LT_Y_ctrl, Animal A51, Frontal_cortex

description:
RNAseq batch3
A51_FCTX


title: H144_ALVAC_wk12

value: F


title: DFMF_ALVAC_wk36

value: DFMF

value: M


title: M36_DNA_wk12

value: DNA group

value: DNA


title: LT_Y_ctrl, Animal A51, Adipose_tissue

description:
RNAseq batch3
A51_Adipose


title: LT_Y_ctrl, Animal A51, Kidney

description:
RNAseq batch3
A51_Kid

value: Kidney


title: B13_Adipose

description:
B13
208114950054_R03C02


title: H305_ALVAC_pre

value: ALVAC group

value: ALVAC


title: M94_ALVAC_wk12


title: LT_A_ctrl, Animal B37, Frontal_cortex

description:
RNAseq batch3
B37_FCTX


title: M52_DNA_wk12


title: H143_DNA_wk12


title: DFGK_DNA_pre

value: DFGK

value: Pre Vacc


title: LT_A_ctrl, Animal B37, Adipose_tissue

description:
RNAseq batch3
B37_Adipose


title: B28_FCTX

description:
B28
208114950054_R02C02

value: FCTX


title: LT_A_Ex, Animal B36, Skeletal_muscle

description:
RNAseq batch3
B36_SkeletalMuscle


title: M50_DNA_pre


title: B13_FCTX

description:
B13
208114950054_R01C02


title: DFFW_DNA_pre

value: DFFW


title: DFGC_DNA_pre

value: DFGC


title: LT_A_Ex, Animal B36, Spleen

description:
RNAseq batch3
B36_Spleen

value: Spleen


title: B13_Hippo

description:
B13
208114950054_R05C01

value: Hippo


title: DFKT_ALVAC_pre

value: DFKT


title: B28_Hippo

description:
B28
208114950054_R06C01


title: B28_Adipose

description:
B28
208114950054_R04C02

value: Adipose


title: LT_A_Ex, Animal B36, Lung

description:
RNAseq batch3
B36_Lung

value: Lung


title: MRL_DNA_wk36

value: MRL

value: F


title: DEMI_DNA_wk12

value: DEMI

value: M

value: DNA group


title: DFMF_ALVAC_pre

value: DFMF

value: ALVAC group


title: B34_Colon

description:
B34
208114950054_R04C01

value: Colon


title: M50_DNA_wk36

value: DNA


title: LT_A_Ex, Animal B36, Liver

description:
RNAseq batch3
B36_Liver

value: Liver


title: B15_Colon

description:
B15
208114950054_R03C01


title: M94_ALVAC_pre

value: Pre Vacc

value: ALVAC


title: DFNF_ALVAC_wk12

value: DFNF


title: LT_A_Ex, Animal B36, Kidney

description:
RNAseq batch3
B36_Kid

value: Kidney


title: DFAW_ALVAC_wk36

value: DFAW


title: B34_Adipose

description:
B34
208114950054_R02C01

value: Adipose


title: DFGF_DNA_wk36

value: DFGF


title: LT_A_Ex, Animal B36, Hippocampus

description:
RNAseq batch3
B36_Hipp

value: Hippocampus


title: M91_DNA_pre

value: F


title: DFER_ALVAC_wk36

value: DFER


title: DFIR_DNA_wk12

value: DFIR

value: M


title: B15_Adipose

description:
B15
208114950054_R01C01


title: LT_A_Ex, Animal B36, Heart

description:
RNAseq batch3
B36_Heart

value: Heart


title: H299_DNA_pre

value: DNA group


title: B34_FCTX

description:
B34
208114950013_R06C02

value: FCTX


title: MRP_DNA.control_wk36

value: MRP

value: Controls challenged with DNA group

value: DNA control


title: B15_FCTX

description:
B15
208114950013_R05C02


title: MRD_ALVAC_wk36

value: MRD

value: ALVAC group

value: ALVAC


title: LT_A_Ex, Animal B36, Hypothalamus

description:
RNAseq batch3
B36_HTH

value: Hypothalamus


title: B34_Hippo

description:
B34
208114950013_R04C02

value: Hippo


title: DEZV_DNA.control_pre

value: DEZV

value: Pre Vacc


title: DF49_ALVAC_pre


title: DFNF_ALVAC_wk36

value: DFNF


title: LT_A_Ex, Animal B36, Frontal_cortex

description:
RNAseq batch3
B36_FCTX


title: DEVV_DNA_wk36

value: DEVV

value: DNA


title: M48_ALVAC_wk12

value: F


title: B16_Colon

description:
B16
208114950013_R01C02

value: Colon


title: B15_Hippo

description:
B15
208114950013_R03C02


title: M83_ALVAC_pre


title: A55_Colon

description:
A55
208114950013_R02C02


title: LT_A_Ex, Animal B36, Adipose_tissue

description:
RNAseq batch3
B36_Adipose


title: DFGL_ALVAC_wk12

value: DFGL

value: M


title: H144_ALVAC_wk36


title: LT_A_Ex, Animal B30, Skeletal_muscle

description:
RNAseq batch3
B30_SkeletalMuscle


title: LT_A_Ex, Animal B30, Spleen

description:
RNAseq batch3
B30_Spleen

value: Spleen


title: A55_Adipose

description:
A55
208114950013_R06C01

value: Adipose


title: DFLG_DNA_wk36

value: DFLG

value: DNA group


title: DFNA_ALVAC_pre

value: DFNA

value: ALVAC group


title: LT_A_Ex, Animal B36, Colon

description:
RNAseq batch3
B36_Colon


title: A51_Adipose

description:
A51
208114950013_R05C01


title: LT_A_Ex, Animal B30, Lung

description:
RNAseq batch3
B30_Lung

value: Lung


title: DFIA_ALVAC_wk12

value: DFIA

value: ALVAC


title: LT_A_Ex, Animal B30, Liver

description:
RNAseq batch3
B30_Liver

value: Liver


title: A55_FCTX

description:
A55
208114950013_R04C01

value: FCTX


title: DFIA_ALVAC_pre

value: Pre Vacc


title: DEMI_DNA_pre

value: DEMI

value: DNA


title: DFCD_DNA_wk36

value: DFCD


title: LT_A_Ex, Animal B30, Hippocampus

description:
RNAseq batch3
B30_Hipp

value: Hippocampus


title: LT_A_Ex, Animal B30, Kidney

description:
RNAseq batch3
B30_Kid

value: Kidney


title: 045_ALVAC_wk36

value: F


title: A55_Hippo

description:
A55
208114950013_R02C01

value: Hippo


title: DEZW_DNA_wk12

value: DEZW

value: M


title: 00B_ALVAC.control_wk12

value: Controls challenged with ALVAC group

value: ALVAC control


title: LT_A_Ex, Animal B30, Heart

description:
RNAseq batch3
B30_Heart

value: Heart


title: DFIR_DNA_pre

value: DFIR

value: DNA group


title: A44_CardiacMuscle

description:
A44
208114950111_R06C02

source_name: CardiacMuscle

value: CardiacMuscle


title: A51_FCTX

description:
A51
208114950013_R03C01

value: FCTX


title: A51_Hippo

description:
A51
208114950013_R01C01


title: M50_DNA_wk12


title: LT_A_Ex, Animal B30, Hypothalamus

description:
RNAseq batch3
B30_HTH

value: Hypothalamus


title: A46_SkeletalMuscle

description:
A46
208114950111_R05C02

source_name: SkeletalMuscle

value: SkeletalMuscle


title: LT_A_Ex, Animal B28, Lung

description:
RNAseq batch2
B28_lung

value: Lung


title: LT_A_Ex, Animal B28, Heart

description:
RNAseq batch2
B28_heart


title: DFAN_DNA_wk36

value: DFAN

value: DNA


title: A44_SkeletalMuscle

description:
A44
208114950111_R04C02


title: BXD90 HFD

type: RNA

city: Lausanne

first: Xiaoxu

last: Li

address: Station 15 - CH

country: Switzerland

institute: EPFL

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD90 mice fed on high fat diet

hyb_protocol: Labeled cDNA was hybridized on an Affymetrix Clariom S Assay microarray platform (GPL23038) in ~16 hours of incubation, then washed and stained using an Affymetrix 450 Fluidics Station according to Affymetrix protocols.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner.

data_processing: Intensities were processed using the apt-probeset-summarize script from the Array Power Tool suite (version 2.11.3, https://downloads.thermofisher.com/APT/APT_2.11.3/apt_2.11.3_linux_64_bit_x86_binaries.zip) with the gc-sst-rma-sketch standard method. Data processing code deposited at https://doi.org/10.5281/zenodo.4899683.

label: biotin

source_name: proximal colon, high-fat diet

label_protocol: 100ng of total RNA was amplified using the Ambion® WT Expression Kit from life technologies (part number 4411974) and 5,500ng of cDNA was fragmented and labeled using the Affymetrix WT terminal labeling kit (part number 900671) all following manufacturers protocols

growth_protocol: In groups of 3-5 animals from same strain and under same diet, in isolator cages with individual air filtration (500 cm2, GM500, Tecniplast) and provided water ad libitum

extract_protocol: A ~1 cm portion of the proximal half part of the colon was excised following euthanasia and immediately stored in liquid nitrogen. Total RNA was extracted using trizol. RNA concentration was assessed using a Nanodrop and RNA integrity was assessed using a Bioanalyzer. RNA extracts from approximately 5 animals of the same strain fed the same diet, were pooled at equal mass concentration and cleaned up using the Qiagen RNEasy kit.

treatment_protocol: Mice were fed CD ad libitum until 8 weeks of age. From 8 weeks to 29 weeks, half of the cohort was fed ad libitum HFD and the rest continued to be fed a CD. CD: 24% kCal of protein, 18% kCal of fat, 58% kCal of carbohydrate – Envigo, Indianapolis, USA, HFD: 18.3% kCal of protein, 60.3% kCal of fat, 21.4% kCal of carbohydrate – Envigo, Indianapolis, USA

value: 29 weeks

value: Male

value: Proximal colon

value: HFD

value: high fat diet

value: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks until heuthanasia, mice were then fed a high-fat diet (HFD) ad libitum.

value: Teklad Custom Diet TD.06414


title: DBA/2J HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male DBA/2J mice fed on high fat diet

value: 18.3% kCal of protein, 60.3% kCal of fat, 21.4% kCal of carbohydrate


title: LT_A_Ex, Animal B28, Colon

description:
RNAseq batch2
B28_colon

value: Colon


title: A47_SkeletalMuscle

description:
A47
208114950111_R03C02


title: C57BL/6J HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male C57BL/6J mice fed on high fat diet


title: BXD87 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD87 mice fed on high fat diet


title: BXD89 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD89 mice fed on high fat diet


title: BXD84 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD84 mice fed on high fat diet


title: BXD81 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD81 mice fed on high fat diet


title: BXD79 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD79 mice fed on high fat diet


title: H216_DNA_wk12

value: F

value: DNA group


title: A46_Colon

description:
A46
208114950111_R02C02


title: DFGK_DNA_wk36

value: DFGK

value: M


title: A44_Colon

description:
A44
208114950111_R01C02


title: LT_A_Ex, Animal B28, Spleen

description:
RNAseq batch2
B28_spleen

value: Spleen


title: A43_Hippo

description:
A43
208114950111_R05C01

value: Hippo


title: DETE_ALVAC_wk12

value: DETE

value: ALVAC group

value: ALVAC


title: A46_Hippo

description:
A46
208114950111_R06C01


title: H304_ALVAC_wk36


title: LT_A_ctrl, Animal B27, Lung

description:
RNAseq batch2
B27_lung

value: Lung


title: DFGF_DNA_pre

value: DFGF

value: Pre Vacc

value: DNA


title: DFMF_ALVAC_wk12

value: DFMF


title: LT_A_ctrl, Animal B27, Spleen

description:
RNAseq batch2
B27_spleen


title: E28_SkeletalMuscle

description:
E28
208114950111_R03C01

value: SkeletalMuscle


title: E10_CardiacMuscle

description:
E10
208114950111_R04C01

value: CardiacMuscle


title: DFGZ_ALVAC.control_pre

value: DFGZ

value: Controls challenged with ALVAC group

value: ALVAC control


title: LT_A_ctrl, Animal B27, Colon

description:
RNAseq batch2
B27_colon

value: Colon


title: LT_A_ctrl, Animal B27, Heart

description:
RNAseq batch2
B27_heart

value: Heart


title: LT_A_Ex, Animal B28, Adipose_tissue

description:
RNAseq batch2
B28_adipose


title: M46_ALVAC_wk12

value: F


title: E10_SkeletalMuscle

description:
E10
208114950111_R02C01


title: BXD75 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD75 mice fed on high fat diet

value: 29 weeks

value: Male

value: Proximal colon

value: HFD

value: high fat diet

value: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks until heuthanasia, mice were then fed a high-fat diet (HFD) ad libitum.

value: 18.3% kCal of protein, 60.3% kCal of fat, 21.4% kCal of carbohydrate

value: Teklad Custom Diet TD.06414


title: BXD73 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD73 mice fed on high fat diet


title: BXD67 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD67 mice fed on high fat diet


title: BXD69 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD69 mice fed on high fat diet


title: BXD64 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD64 mice fed on high fat diet


title: BXD62 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD62 mice fed on high fat diet


title: BXD66 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD66 mice fed on high fat diet


title: E36_SkeletalMuscle

description:
E36
208114950111_R01C01


title: LT_A_Ex, Animal B26, Spleen

description:
RNAseq batch2
B26_spleen

value: Spleen


title: E28_Colon

description:
E28
208114950108_R06C02


title: LT_A_Ex, Animal B26, Lung

description:
RNAseq batch2
B26_lung

value: Lung


title: DFKT_ALVAC_wk36

value: DFKT

value: M

value: ALVAC group

value: ALVAC


title: E10_Colon

description:
E10
208114950108_R05C02

value: Colon


title: LT_A_Ex, Animal B26, Heart

description:
RNAseq batch2
B26_heart

value: Heart


title: DFAP_ALVAC_wk36

value: DFAP


title: LT_A_ctrl, Animal B27, Adipose_tissue

description:
RNAseq batch2
B27_adipose


title: LT_A_Ex, Animal B26, Adipose_tissue

description:
RNAseq batch2
B26_adipose


title: E28_Hippo

description:
E28
208114950108_R04C02

value: Hippo


title: 00B_ALVAC.control_pre

value: F

value: Controls challenged with ALVAC group

value: Pre Vacc

value: ALVAC control


title: E6_Hippo [208114950108_R03C02]

description:
E6
208114950108_R03C02


title: E15_CardiacMuscle

description:
E15
208114950108_R02C02

value: CardiacMuscle


title: M34_DNA.control_wk36

value: Controls challenged with DNA group

value: DNA control


title: DEZW_DNA_wk36

value: DEZW

value: DNA group

value: DNA


title: LT_A_Ex, Animal B25, Spleen

description:
RNAseq batch2
B25_spleen

value: Spleen


title: DFHC_DNA_wk36

value: DFHC

value: M


title: M44_DNA_wk12


title: LT_A_Ex, Animal B25, Lung

description:
RNAseq batch2
B25_lung

value: Lung


title: LT_A_Ex, Animal B26, Colon

description:
RNAseq batch2
B26_colon

value: Colon


title: E33_SkeletalMuscle

description:
E33
208114950108_R01C02

value: SkeletalMuscle


title: LT_A_Ex, Animal B25, Heart

description:
RNAseq batch2
B25_heart

value: Heart


title: MRL_DNA_pre

value: MRL

value: F


title: E15_SkeletalMuscle

description:
E15
208114950108_R06C01


title: LT_A_Ex, Animal B25, Colon

description:
RNAseq batch2
B25_colon


title: M46_ALVAC_pre

value: ALVAC group

value: Pre Vacc

value: ALVAC


title: E34_SkeletalMuscle

description:
E34
208114950108_R05C01


title: DFNB_ALVAC.control_wk36

value: DFNB

value: Controls challenged with ALVAC group

value: ALVAC control


title: LT_A_Ex, Animal B25, Adipose_tissue

description:
RNAseq batch2
B25_adipose


title: BXD55 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD55 mice fed on high fat diet

value: 29 weeks

value: Male

value: Proximal colon

value: HFD

value: high fat diet

value: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks until heuthanasia, mice were then fed a high-fat diet (HFD) ad libitum.

value: 18.3% kCal of protein, 60.3% kCal of fat, 21.4% kCal of carbohydrate

value: Teklad Custom Diet TD.06414


title: E33_Colon

description:
E33
208114950108_R04C01

value: Colon


title: DFAP_ALVAC_wk12

value: DFAP

value: M


title: BXD51 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD51 mice fed on high fat diet


title: LT_A_ctrl, Animal B24, Spleen

description:
RNAseq batch2
B24_spleen

value: Spleen


title: E15_Colon

description:
E15
208114950108_R03C01


title: M94_ALVAC_wk36

value: F

value: ALVAC group


title: LT_A_ctrl, Animal B24, Lung

description:
RNAseq batch2
B24_lung

value: Lung


title: BXD48 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD48 mice fed on high fat diet


title: BXD45 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD45 mice fed on high fat diet


title: BXD48a HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD48a mice fed on high fat diet


title: BXD49 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD49 mice fed on high fat diet


title: BXD34 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD34 mice fed on high fat diet


title: BXD39 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD39 mice fed on high fat diet


title: BXD43 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD43 mice fed on high fat diet


title: E33_Hippo

description:
E33
208114950108_R02C01

value: Hippo


title: BXD40 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD40 mice fed on high fat diet


title: LT_A_ctrl, Animal B24, Heart

description:
RNAseq batch2
B24_heart

value: Heart


title: E15_Hippo

description:
E15
208114950108_R01C01


title: LT_A_ctrl, Animal B24, Colon

description:
RNAseq batch2
B24_colon


title: DEZW_DNA_pre

value: DEZW

value: DNA group

value: Pre Vacc

value: DNA


title: E25_SkeletalMuscle

description:
E25
208114950107_R05C02

value: SkeletalMuscle


title: E7_CardiacMuscle

description:
E7
208114950107_R06C02

value: CardiacMuscle


title: LT_A_ctrl, Animal B24, Adipose_tissue

description:
RNAseq batch2
B24_adipose


title: LT_A_ctrl, Animal B15, Spleen

description:
RNAseq batch2
B15_spleen


title: M88_DNA_wk12


title: E7_SkeletalMuscle

description:
E7
208114950107_R04C02


title: DFNB_ALVAC.control_wk12

value: DFNB

value: Controls challenged with ALVAC group

value: ALVAC control


title: DFRF_DNA.control_pre

value: DFRF

value: Controls challenged with DNA group

value: DNA control


title: E31_SkeletalMuscle

description:
E31
208114950107_R03C02


title: LT_A_ctrl, Animal B15, Lung

description:
RNAseq batch2
B15_lung


title: H299_DNA_wk36

value: F


title: LT_A_ctrl, Animal B15, Heart

description:
RNAseq batch2
B15_heart


title: E25_Colon

description:
E25
208114950107_R02C02

value: Colon


title: BXD12 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD12 mice fed on high fat diet

value: 29 weeks

value: Male

value: Proximal colon

value: HFD

value: high fat diet

value: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks until heuthanasia, mice were then fed a high-fat diet (HFD) ad libitum.

value: 18.3% kCal of protein, 60.3% kCal of fat, 21.4% kCal of carbohydrate

value: Teklad Custom Diet TD.06414


title: LT_A_ctrl, Animal B15, Colon

description:
RNAseq batch2
B15_colon


title: BXD27 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD27 mice fed on high fat diet


title: E7_Colon

description:
E7
208114950107_R01C02


title: BXD11 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD11 mice fed on high fat diet


title: BXD8 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD8 mice fed on high fat diet


title: BXD32 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD32 mice fed on high fat diet


title: BXD6 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD6 mice fed on high fat diet


title: BXD1 HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD1 mice fed on high fat diet


title: 036_DNA_pre

value: DNA group

value: Pre Vacc

value: DNA


title: LT_A_ctrl, Animal B15, Adipose_tissue

description:
RNAseq batch2
B15_adipose


title: M44_DNA_wk36


title: E25_Hippo

description:
E25
208114950107_R06C01

value: Hippo


title: DBA/2J CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male DBA/2J mice fed on chow diet

source_name: proximal colon, chow diet

value: CD

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: 4% kCal of protein, 18% kCal of fat, 58% kCal of carbohydrate

value: Teklad Global 18% Protein Rodent Diet 2018


title: C57BL/6J CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male C57BL/6J mice fed on chow diet

value: 29 weeks


title: M34_DNA.control_wk12

value: F

value: Controls challenged with DNA group

value: DNA control


title: LT_A_Ex, Animal B14, Lung

description:
RNAseq batch2
B14_lung

value: Lung


title: DEGI_DNA_wk36

value: DEGI

value: M


title: E7_Hippo

description:
E7
208114950107_R05C01


title: E9_CardiacMuscle

description:
E9
208114950107_R04C01

value: CardiacMuscle


title: DEWC_ALVAC_pre

value: DEWC

value: ALVAC group

value: ALVAC


title: BXD90 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD90 mice fed on chow diet

value: Male

value: Proximal colon


title: E21_SkeletalMuscle

description:
E21
208114950107_R03C01

value: SkeletalMuscle


title: LT_A_Ex, Animal B14, Heart

description:
RNAseq batch2
B14_heart

value: Heart


title: BXD87 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD87 mice fed on chow diet

value: CD

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: 4% kCal of protein, 18% kCal of fat, 58% kCal of carbohydrate


title: 045_ALVAC_wk12

value: F


title: BXD84 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD84 mice fed on chow diet

value: 29 weeks

value: Teklad Global 18% Protein Rodent Diet 2018


title: LT_A_Ex, Animal B14, Colon

description:
RNAseq batch2
B14_colon

value: Colon


title: E9_SkeletalMuscle

description:
E9
208114950107_R02C01


title: MRP_DNA.control_pre

value: MRP

value: Controls challenged with DNA group

value: Pre Vacc

value: DNA control


title: DFFM_ALVAC_wk36

value: DFFM

value: M

value: ALVAC group

value: ALVAC


title: E35_SkeletalMuscle

description:
E35
208114950107_R01C01

value: SkeletalMuscle


title: E21_Colon

description:
E21
208114950106_R06C02


title: DFHC_DNA_pre

value: DFHC

value: DNA group

value: DNA


title: LT_A_Ex, Animal B14, Adipose_tissue

description:
RNAseq batch2
B14_adipose


title: LT_A_Ex, Animal B13, Spleen

description:
RNAseq batch2
B13_spleen

source_name: Spleen

value: Spleen


title: DFGC_DNA_wk12

value: DFGC


title: LT_A_Ex, Animal B14, Spleen

description:
RNAseq batch2
B14_spleen


title: LT_A_Ex, Animal B13, Lung

description:
RNAseq batch2
B13_lung

source_name: Lung

value: Lung


title: BXD81 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD81 mice fed on chow diet

value: 29 weeks

value: Male

value: Proximal colon

value: CD

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: 4% kCal of protein, 18% kCal of fat, 58% kCal of carbohydrate

value: Teklad Global 18% Protein Rodent Diet 2018


title: E9_Colon

description:
E9
208114950106_R05C02

value: Colon


title: DFJP_ALVAC.control_pre

value: DFJP

value: M

value: Controls challenged with ALVAC group

value: Pre Vacc

value: ALVAC control


title: E21_Hippo

description:
E21
208114950106_R04C02

source_name: Hippo

value: Hippo


title: LT_A_Ex, Animal B13, Heart

description:
RNAseq batch2
B13_heart

value: Heart


title: H305_ALVAC_wk12

value: F

value: ALVAC group

value: ALVAC


title: LT_A_Ex, Animal B13, Colon

description:
RNAseq batch2
B13_colon


title: E9_Hippo

description:
E9
208114950106_R03C02


title: LT_A_Ex, Animal B13, Adipose_tissue

description:
RNAseq batch2
B13_adipose


title: DFCD_DNA_wk12

value: DFCD

value: DNA group

value: DNA


title: DFGL_ALVAC_pre

value: DFGL


title: LT_Y_ctrl, Animal A58, Spleen

description:
RNAseq batch2
A58_spleen

value: Spleen


title: E30_SkeletalMuscle

description:
E30
208114950106_R01C02

value: SkeletalMuscle


title: 00B_ALVAC.control_wk36


title: E23_SkeletalMuscle

description:
E23
208114950106_R06C01


title: LT_Y_ctrl, Animal A58, Heart

description:
RNAseq batch2
A58_heart


title: BXD89 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD89 mice fed on chow diet

value: 29 weeks

value: Male

value: Proximal colon

value: CD

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: 4% kCal of protein, 18% kCal of fat, 58% kCal of carbohydrate

value: Teklad Global 18% Protein Rodent Diet 2018


title: BXD79 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD79 mice fed on chow diet


title: E32_SkeletalMuscle

description:
E32
208114950106_R05C01


title: H306_ALVAC.control_wk36

value: F

value: Controls challenged with ALVAC group

value: ALVAC control


title: LT_Y_ctrl, Animal A58, Adipose_tissue

description:
RNAseq batch2
A58_adipose


title: DFNA_ALVAC_wk12

value: DFNA

value: M

value: ALVAC group

value: ALVAC


title: BXD75 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD75 mice fed on chow diet


title: LT_Y_ctrl, Animal A57, Spleen

description:
RNAseq batch2
A57_spleen

value: Spleen


title: BXD66 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD66 mice fed on chow diet


title: BXD69 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD69 mice fed on chow diet


title: BXD73 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD73 mice fed on chow diet


title: BXD67 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD67 mice fed on chow diet


title: E23_Colon

description:
E23
208114950106_R03C01

value: Colon


title: E23_CardiacMuscle

description:
E23
208114950106_R02C02

value: CardiacMuscle


title: E30_Colon

description:
E30
208114950106_R04C01


title: BXD64 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD64 mice fed on chow diet

value: 29 weeks

value: Male


title: BXD62 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD62 mice fed on chow diet

value: Proximal colon

value: CD


title: DFIR_DNA_wk36

value: DFIR

value: DNA group

value: DNA


title: LT_Y_ctrl, Animal A57, Lung

description:
RNAseq batch2
A57_lung

value: Lung


title: E30_Hippo

description:
E30
208114950106_R02C01

value: Hippo


title: LT_Y_ctrl, Animal A58, Lung

description:
RNAseq batch2
A58_lung


title: M83_ALVAC_wk36

value: F


title: LT_Y_ctrl, Animal A57, Heart

description:
RNAseq batch2
A57_heart

value: Heart


title: E23_Hippo

description:
E23
208114950106_R01C01


title: LT_Y_ctrl, Animal A57, Colon

description:
RNAseq batch2
A57_colon


title: H216_DNA_pre

value: Pre Vacc


title: M48_ALVAC_wk36

value: ALVAC group


title: A45_SkeletalMuscle

description:
A45
208114950104_R05C02

value: SkeletalMuscle


title: BXD51 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD51 mice fed on chow diet

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: 4% kCal of protein, 18% kCal of fat, 58% kCal of carbohydrate

value: Teklad Global 18% Protein Rodent Diet 2018


title: BXD48a CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD48a mice fed on chow diet

value: 29 weeks

value: Male


title: A42_CardiacMuscle

description:
A42
208114950104_R06C02

value: CardiacMuscle


title: LT_Y_ctrl, Animal A57, Adipose_tissue

description:
RNAseq batch2
A57_adipose


title: LT_Y_ctrl, Animal A56, Spleen

description:
RNAseq batch2
A56_spleen

value: Spleen


title: LT_Y_ctrl, Animal A56, Lung

description:
RNAseq batch2
A56_lung


title: M48_ALVAC_pre

value: ALVAC


title: M34_DNA.control_pre

value: Controls challenged with DNA group

value: DNA control


title: A47_Colon

description:
A47
208114950104_R03C02

value: Colon


title: H299_DNA_wk12

value: F

value: DNA group

value: DNA


title: A42_SkeletalMuscle

description:
A42
208114950104_R04C02


title: H305_ALVAC_wk36

value: ALVAC group


title: A43_Colon

description:
A43
208114950104_R02C02


title: H144_ALVAC_pre

value: Pre Vacc


title: LT_Y_ctrl, Animal A56, Colon

description:
RNAseq batch2
A56_colon


title: BXD45 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD45 mice fed on chow diet

value: Proximal colon

value: CD

value: chow diet


title: BXD48 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD48 mice fed on chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: 4% kCal of protein, 18% kCal of fat, 58% kCal of carbohydrate

value: Teklad Global 18% Protein Rodent Diet 2018


title: BXD55 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD55 mice fed on chow diet

value: 29 weeks

value: Male


title: A42_Colon

description:
A42
208114950104_R01C02


title: BXD49 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD49 mice fed on chow diet


title: LT_Y_ctrl, Animal A56, Adipose_tissue

description:
RNAseq batch2
A56_adipose


title: DFER_ALVAC_wk12

value: DFER

value: M

value: ALVAC


title: BXD40 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD40 mice fed on chow diet


title: A45_Hippo

description:
A45
208114950104_R06C01

value: Hippo


title: M46_ALVAC_wk36

value: F


title: E6_CardiacMuscle

description:
E6
208114950104_R04C01

value: CardiacMuscle


title: LT_Y_ctrl, Animal A55, Spleen

description:
RNAseq batch2
A55_spleen

value: Spleen


title: LT_Y_ctrl, Animal A55, Lung

description:
RNAseq batch2
A55_lung

value: Lung


title: LT_Y_ctrl, Animal A55, Heart

description:
RNAseq batch2
A55_heart

value: Heart


title: MRL_DNA_wk12

value: MRL

value: DNA group

value: DNA


title: LT_Y_ctrl, Animal A56, Heart

description:
RNAseq batch2
A56_heart


title: H306_ALVAC.control_pre

value: Controls challenged with ALVAC group

value: Pre Vacc

value: ALVAC control


title: E22_SkeletalMuscle

description:
E22
208114950104_R03C01

value: SkeletalMuscle


title: LT_Y_ctrl, Animal A55, Colon

description:
RNAseq batch2
A55_colon

value: Colon


title: BXD32 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD32 mice fed on chow diet

value: 29 weeks

value: Male

value: Proximal colon

value: CD

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: 4% kCal of protein, 18% kCal of fat, 58% kCal of carbohydrate

value: Teklad Global 18% Protein Rodent Diet 2018


title: BXD39 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD39 mice fed on chow diet


title: A42_Hippo

description:
A42
208114950104_R05C01

value: Hippo


title: BXD11 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD11 mice fed on chow diet


title: E6_SkeletalMuscle

description:
E6
208114950104_R02C01


title: LT_Y_ctrl, Animal A55, Adipose_tissue

description:
RNAseq batch2
A55_adipose


title: MRR_ALVAC_pre

value: MRR

value: F

value: ALVAC group

value: ALVAC


title: BXD12 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD12 mice fed on chow diet


title: BXD43 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD43 mice fed on chow diet


title: BXD34 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD34 mice fed on chow diet


title: BXD27 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD27 mice fed on chow diet


title: BXD8 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD8 mice fed on chow diet


title: E36_Colon

description:
E36
208114950104_R01C01


title: LT_Y_ctrl, Animal A52, Spleen

description:
RNAseq batch2
A52_spleen

value: Spleen


title: DEWC_ALVAC_wk12

value: DEWC

value: M


title: Zymomonas mobilis WT Anaerobic RNA-seq Replicate C

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description: Library name: ZM4-WT_O2-control-3

data_processing:
All paired-end FASTQ files were processed through the same pipeline. Reads were trimmed using Trimmomatic version 0.3  with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3, SLIDINGWINDOW of 3:30, and MINLEN of 36. After trimming, the reads were aligned to the Z. mobilis ZM4 genome sequence (GenBank accession GCF_003054575.1) using bwa-mem (version 0.7.17-h5bf99c6_8)  with default settings. Alignment files were further processed with Picard-tools (version 2.26.10) (https://broadinstitute.github.io/picard/) (CleanSAM and AddOrRepleaceReadGroups commands) and samtools (version 1.2)  (sort and index commands). Paired aligned reads were mapped to gene locations using HTSeq version 0.6.0. The R package edgeR (version 3.30.3) with default settings was used to identify significantly differentially expressed genes from pairwise analyses, using Benjamini and Hochberg false discovery rate (FDR) less than 0.05 as a significance threshold (57). Raw sequencing reads were normalized using the fragments per kilobase per million mapped reads method (FPKM).
Assembly: GCF_003054575.1
Supplementary files format and content: 20250627_Kiley_Oxidizing_Stress_RNAseq_HTSeq_raw_counts.txt contains the RAW gene counts for the experiments as determined by Htseq-count
Supplementary files format and content: 20250627_Kiley_Oxidizing_Stress_RNAseq_FKPM_normalized_counts.txt contains FPKM normalized gene counts for all experiments.

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

source_name: bacterial cell

growth_protocol: Strains were grown in ZRDM medium, a modification of Neidhardt medium buffered with 80 mM MES to pH 6.0, and supplemented with a mixture of amino acids (5x supplement EZ, Teknova) and nucleosides (10x ACGU Solution, Teknova). For iron experiments, no iron was added to the media, and the overnight cultures (used to initiate the growth) were growth in the same media with lower Fe concentration (1µM FeSO4). Cultures were growth under anaerobic conditions (95% N2, 5% CO2) by bubbling the gas mixtures into the culture. All culture were incubated at 30º C. The overnigt cultures used to inoculate the cultures were grown under anaerobic conditions.

extract_protocol:
The RNA was extracted, the same day as the cells were harvest, following standard hot phenol:chlorofom protocol, and ethanol precipitated overnight at -80º C. The RNA then was resuspended in RNase free water and treated with DNAse I at 37ºC for 1 hour and then clean using Monarch® Spin RNA Cleanup Kit (T20240L, NEB)
rRNA in the samples was depleted using the QIAseq FastSelect 5S/16S/23S, rRNA Plant, rRNA Yeast and custom rRNA Algae depletion Kits (Qiagen, Hilden, Germany). RNA-seq library preparation and sequencing was performed by the Joint Genome Institute (JGI) using default parameters. rRNA in the samples was depleted using the QIAseq FastSelect kit (Qiagen, Hilden, Germany). Libraries were constructed using the TruSeq stranded mRNA kit (Illumina) following standard JGI protocols.

treatment_protocol: Cells were grown under anaerobic conditions, until OD600 = 0.4 - 0.6. Then, the following treatmets were added: 15 µM H2O2  or  1.5 µM Paraquat plus O2 (70% N2, 25% O2, 5% CO2) (O2 was also added to the control cultures). For cultures grown without Fe 5 µM α, α’- dipyridyl (DIP) was added. The treatment was mainteined for 20 min before the cells were harvested by collecting 10 mL of cells over 1 mL cold 5% vol/vol phenol:ethanol mixture. Deletion strains were harvested once the reached the desired OD without further treament.

tag: replicate

value: C

tag: cell type

value: bacterial cell

value: WT

tag: oxygen level

value: anaerobic

tag: oxidative stress


title: M44_DNA_pre

value: DNA group

value: Pre Vacc

value: DNA


title: DEWC_ALVAC_wk36


title: E6_Colon

description:
E6
208114950102_R05C02

tag: tissue

value: Colon


title: Zymomonas mobilis WT Anaerobic RNA-seq Replicate B

description: Library name: ZM4-WT_O2-control-2

value: B


title: LT_Y_ctrl, Animal A52, Lung

description:
RNAseq batch2
A52_lung

value: Lung


title: E22_Hippo

description:
E22
208114950102_R04C02

value: Hippo


title: DFNA_ALVAC_wk36

value: DFNA


title: LT_Y_ctrl, Animal A52, Heart

description:
RNAseq batch2
A52_heart

value: Heart


title: Zymomonas mobilis WT Anaerobic RNA-seq Replicate A

description: Library name: ZM4-WT_O2-control-1

value: A


title: M91_DNA_wk36

value: F


title: BXD1 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD1 mice fed on chow diet

tag: age

value: 29 weeks

value: Male

value: Proximal colon

value: CD

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: 4% kCal of protein, 18% kCal of fat, 58% kCal of carbohydrate

value: Teklad Global 18% Protein Rodent Diet 2018


title: BXD6 CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD6 mice fed on chow diet


title: LT_Y_ctrl, Animal A52, Colon

description:
RNAseq batch2
A52_colon


title: E22_Colon

description:
E22
208114950102_R06C02


title: E6_Hippo

description:
E6
208114950102_R03C02


title: LT_Y_ctrl, Animal A52, Adipose_tissue

description:
RNAseq batch2
A52_adipose


title: E12_CardiacMuscle

description:
E12
208114950102_R02C02

value: CardiacMuscle


title: DFLG_DNA_wk12

value: DFLG

value: M

value: DNA group

value: DNA


title: LT_A_ctrl, Animal B39, Spleen

description:
RNAseq batch2
B39_spleen

value: Spleen


title: Zymomonas mobilis WT Aerobic RNA-seq Replicate A

description: Library name: ZM4-WT_O2+control-1

value: bacterial cell

value: WT

value: aerobic


title: Zymomonas mobilis WT Aerobic RNA-seq Replicate B

description: Library name: ZM4-WT_O2+control-2

value: B


title: DEZV_DNA.control_wk12

value: DEZV

value: Controls challenged with DNA group

value: DNA control


title: Zymomonas mobilis WT Aerobic RNA-seq Replicate C

description: Library name: ZM4-WT_O2+control-3

value: C


title: E12_SkeletalMuscle

description:
E12
208114950102_R06C01

value: SkeletalMuscle


title: 01F_ALVAC_wk12

value: F

value: ALVAC group

value: ALVAC


title: LT_A_ctrl, Animal B39, Lung

description:
RNAseq batch2
B39_lung

value: Lung


title: DFAW_ALVAC_wk12

value: DFAW

value: M


title: Zymomonas mobilis WT Anaerobic plus Hydorgen Peroxide RNA-seq Replicate C

description: Library name: ZM4-WT_H2O2-3

value: anaerobic


title: E34_Colon

description:
E34
208114950102_R05C01

value: Colon


title: LT_A_ctrl, Animal B39, Heart

description:
RNAseq batch2
B39_heart

value: Heart


title: Zymomonas mobilis WT Anaerobic plus Hydorgen Peroxide RNA-seq Replicate B

description: Library name: ZM4-WT_H2O2-2

value: bacterial cell

value: WT


title: LT_A_ctrl, Animal B39, Colon

description:
RNAseq batch2
B39_colon


title: E16_Colon

description:
E16
208114950102_R04C01


title: DFJP_ALVAC.control_wk36

value: DFJP

value: Controls challenged with ALVAC group

value: ALVAC control


title: Zymomonas mobilis WT Anaerobic plus Hydorgen Peroxide RNA-seq Replicate A

description: Library name: ZM4-WT_H2O2-1

value: A


title: E12_Colon

description:
E12
208114950102_R03C01


title: LT_A_ctrl, Animal B39, Adipose_tissue

description:
RNAseq batch2
B39_adipose


title: Zymomonas mobilis WT Anaerobic No Iron plus DIP RNA-seq Replicate C

description: Library name: ZM4-WT_NoFe-DIP-3

value: C

value: NoFe-DIP


title: DFKT_ALVAC_wk12

value: DFKT


title: DEWT_DNA.control_wk36

value: DEWT

value: Controls challenged with DNA group

value: DNA control


title: E16_SkeletalMuscle

description:
E16
208114950102_R01C02

value: SkeletalMuscle


title: LT_A_ctrl, Animal B34, Spleen

description:
RNAseq batch2
B34_spleen

value: Spleen


title: E16_Hippo

description:
E16
208114950102_R02C01

value: Hippo


title: Zymomonas mobilis WT Anaerobic No Iron plus DIP RNA-seq Replicate B

description: Library name: ZM4-WT_NoFe-DIP-2

value: B

value: anaerobic


title: LT_A_ctrl, Animal B34, Lung

description:
RNAseq batch2
B34_lung

value: Lung


title: E12_Hippo

description:
E12
208114950102_R01C01


title: DFLG_DNA_pre

value: DFLG

value: M

value: DNA group

value: Pre Vacc

value: DNA


title: Zymomonas mobilis WT Anaerobic No Iron plus DIP RNA-seq Replicate A

description: Library name: ZM4-WT_NoFe-DIP-1

value: A

value: bacterial cell

value: WT


title: E5_CardiacMuscle

description:
E5
208114950101_R06C02

value: CardiacMuscle


title: Zymomonas mobilis WT Anaerobic No Iron RNA-seq Replicate C

description: Library name: ZM4-WT_Control-NoFe-3

value: C

value: Control-NoFe


title: MRD_ALVAC_pre

value: MRD

value: F

value: ALVAC group

value: ALVAC


title: LT_A_ctrl, Animal B34, Heart

description:
RNAseq batch2
B34_heart

value: Heart


title: DEWT_DNA.control_wk12

value: DEWT

value: Controls challenged with DNA group

value: DNA control


title: LT_A_ctrl, Animal B34, Colon

description:
RNAseq batch2
B34_colon

value: Colon


title: Zymomonas mobilis WT Anaerobic No Iron RNA-seq Replicate B

description: Library name: ZM4-WT_Control-NoFe-2

value: B

value: anaerobic


title: LT_A_ctrl, Animal B34, Adipose_tissue

description:
RNAseq batch2
B34_adipose


title: Zymomonas mobilis WT Anaerobic No Iron RNA-seq Replicate A

description: Library name: ZM4-WT_Control-NoFe-1

value: A


title: DFFW_DNA_wk36

value: DFFW

value: M

value: DNA group

value: DNA


title: E5_SkeletalMuscle

description:
E5
208114950101_R04C02

value: SkeletalMuscle


title: E31_Colon

description:
E31
208114950101_R03C02


title: LT_A_ctrl, Animal B39, Circulating_WBCs

description:
RNAseq batch1
B39_WBC_RNA


title: Zymomonas mobilis WT Aerobic plus Paraquat RNA-seq Replicate C

description: Library name: ZM4-WT_PQ-3

value: C

value: bacterial cell

value: WT

value: PQ


title: M83_ALVAC_wk12

value: F

value: ALVAC group

value: ALVAC


title: Zymomonas mobilis WT Aerobic plus Paraquat RNA-seq Replicate B

description: Library name: ZM4-WT_PQ-2


title: LT_A_ctrl, Animal B39, Skeletal_muscle

description:
RNAseq batch1
B39_SkeletalMuscle_RNA


title: E19_Colon

description:
E19
208114950101_R02C02


title: E5_Colon

description:
E5
208114950101_R01C02


title: LT_A_ctrl, Animal B39, Kidney

description:
RNAseq batch1
B39_Kid_RNA

value: Kidney


title: Zymomonas mobilis WT Aerobic plus Paraquat RNA-seq Replicate A

description: Library name: ZM4-WT_PQ-1


title: DFGK_DNA_wk12

value: DFGK


title: LT_A_ctrl, Animal B39, Hippocampus

description:
RNAseq batch1
B39_Hipp_RNA

value: Hippocampus


title: E19_Hippo

description:
E19
208114950101_R06C01

value: Hippo


title: LT_A_ctrl, Animal B39, Hypothalamus

description:
RNAseq batch1
B39_HTH_RNA

value: Hypothalamus


title: Zymomonas mobilis ∆ZMO_0422 Anaerobic RNA-seq Replicate C

description: Library name: ZM4-DrsuR-3

value: anaerobic


title: Zymomonas mobilis ∆ZMO_0422 Anaerobic RNA-seq Replicate B

description: Library name: ZM4-DrsuR-2

value: B


title: E5_Hippo

description:
E5
208114950101_R05C01


title: DEGI_DNA_wk12

value: DEGI

value: M

value: DNA group


title: DFRF_DNA.control_wk36

value: DFRF

value: Controls challenged with DNA group

value: DNA control


title: DETE_ALVAC_pre

value: DETE

value: Pre Vacc


title: E19_SkeletalMuscle

description:
E19
208114950101_R05C02

value: SkeletalMuscle


title: LT_A_ctrl, Animal B39, Frontal_cortex

description:
RNAseq batch1
B39_FCTX_RNA


title: Zymomonas mobilis ∆ZMO_0422 Anaerobic RNA-seq Replicate A

description: Library name: ZM4-DrsuR-1

value: A

value: bacterial cell


title: LT_A_ctrl, Animal B34, Circulating_WBCs

description:
RNAseq batch1
B34_WBC_RNA


title: M61_ALVAC_pre

value: F

value: ALVAC group

value: ALVAC


title: E8_SkeletalMuscle

description:
E8
208114950101_R02C01


title: Zymomonas mobilis ∆ZMO_1411 Anaerobic RNA-seq Replicate C

description: Library name: ZM4-Dfur-3

value: C


title: M52_DNA_wk36

value: DNA


title: DF49_ALVAC_wk12


title: Zymomonas mobilis ∆ZMO_1411 Anaerobic RNA-seq Replicate A

description: Library name: ZM4-Dfur-1

value: anaerobic


title: Zymomonas mobilis ∆ZMO_1411 Anaerobic RNA-seq Replicate B

description: Library name: ZM4-Dfur-2

value: B


title: LT_A_ctrl, Animal B34, Kidney

description:
RNAseq batch1
B34_Kid_RNA

value: Kidney


title: DFJP_ALVAC.control_wk12

value: DFJP

value: M

value: Controls challenged with ALVAC group

value: ALVAC control


title: E35_Colon

description:
E35
208114950101_R01C01

value: Colon


title: H163_DNA_pre

value: DNA group

value: Pre Vacc


title: LT_A_ctrl, Animal B34, Hippocampus

description:
RNAseq batch1
B34_Hipp_RNA

value: Hippocampus


title: Peripheral-blood sorted CART19 cells from BHB-gavaged mice

city: Philadelphia

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Library name: Sample 2
10X Genomics/Azenta

library_source: transcriptomic single cell

data_processing:
The de-multiplexing, barcoding, mapping,  gene coutning, and aggregation was performed using CellRanger (10X; v5.0.1 or higher)
Assembly: GRCh38
Supplementary files format and content: filtered matrix h5 files for input into Seurat, .csv files for Hashtag

source_name: peripheral blood (NSG)

extract_protocol:
Library was prepared according to manufacturers instructions for the 10X Genomics 3' Chemistry GEX. User Guide, CG000315 Revision F was used for library preparation steps. DNA quality was assessed prior to NGS via BioAnalyzer High Sensitivity DNA.
scRNA-seq GEX (gene expression)

treatment_protocol: FACS purified CART19 cells were washed 2x in PBS + 0.04% PBS, and then resuspended in the same solution prior to loading onto 10X Genomics chips.

value: peripheral blood (NSG)

tag: cell line

value: primary T cell


title: E8_Colon

description:
E8
208114950100_R05C02


title: E20_Colon

description:
E20
208114950100_R06C02


title: M91_DNA_wk12

value: F


title: Peripheral-blood sorted CART19 cells from vehicle-gavaged mice

description:
Library name: Sample 1
10X Genomics/Azenta


title: 036_DNA_wk12


title: LT_A_ctrl, Animal B34, Hypothalamus

description:
RNAseq batch1
B34_HTH_RNA

value: Hypothalamus


title: E8_CardiacMuscle

description:
E8
208114950101_R04C01

value: CardiacMuscle


title: E20_Hippo

description:
E20
208114950100_R04C02

value: Hippo


title: LT_A_Ex, Animal B28, Circulating_WBCs

description:
RNAseq batch1
B28_WBC_RNA


title: E20_SkeletalMuscle

description:
E20
208114950101_R03C01

value: SkeletalMuscle


title: E8_Hippo

description:
E8
208114950100_R03C02


title: LT_A_ctrl, Animal B34, Skeletal_muscle

description:
RNAseq batch1
B34_SkeletalMuscle_RNA


title: IMR32_Prex_Dyngo4a_24h_R3

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

description: Library name: IMR32_Prex_Dyngo4a_24h_R3

data_processing:
Sample and read quality were evaluated with FastQC (v0.11.7). The FASTQ files were aligned to the Homo sapiens reference genome (GRCh38.96) using STAR (v2.7.2b).
Post-alignment, read counts were generated and normalized with edgeR (v3.36.0).
PCA plotting confirmed the quality of the data with no outliers shown. Differential expression analysis was performed using the Limma-Voom pipeline (v3.50.3) with four replicates per condition
Assembly: GRCh38.96
Supplementary files format and content: Tab-delimited text file include STAR counts on the forwarded strand per sample

source_name: Brain

growth_protocol: The human neuroblastoma cell lines IMR-32  were grown in RPMI 1640 supplemented with 10% fetal calf serum (FCS), penicillin/streptomycin (100 IU/mL), and L-glutamine (2 mM).

extract_protocol:
RNA isolation was performed using the miRNeasy kit from QIAGEN including an on-column deoxyribonuclease treatment, following manufacturer’s instructions.
total of 200ng of RNA was used as input for the library preparation with the QuantSeq 3′ mRNA library prep kit (Lexogen, Vienna, Austria) with umi barcoding according to the manufacturer’s protocol. Sequencing of the RNA-seq libraries was conducted on the Illumina NextSeq 2000 platform using the NextSeq 2000 P2 Reagents 100 Cycles single-end kit (Illumina #20100981).

treatment_protocol: IMR-32 cells were seeded in T25 culture flasks (Greiner, #690175) at a density of 1.85 × 10⁶ cells per flask and allowed to adhere for 24 hours. Following this, cells were treated with either DMSO or compounds for an additional 24 hours: 2 nM prexasertib (low dose), 1 µM Dyngo-4a (low dose), or 2.26 µM Dyngo-4a (high dose).

value: Brain

value: neuroblast

value: WT

value: Prexasertib + dyngo4a combination


title: LT_A_Ex, Animal B28, Skeletal_muscle

description:
RNAseq batch1
B28_SkeletalMuscle_RNA


title: E13_CardiacMuscle

description:
E13
208114950100_R02C02


title: DEVV_DNA_pre

value: DEVV

value: M

value: DNA


title: DFHC_DNA_wk12

value: DFHC

value: DNA group


title: DEMI_DNA_wk36

value: DEMI


title: E29_SkeletalMuscle

description:
E29
208114950100_R01C02


title: LT_A_Ex, Animal B28, Kidney

description:
RNAseq batch1
B28_Kid_RNA

value: Kidney


title: DFFW_DNA_wk12

value: DFFW


title: IMR32_Prex_Dyngo4a_24h_R1

description: Library name: IMR32_Prex_Dyngo4a_24h_R1


title: LT_A_Ex, Animal B28, Hippocampus

description:
RNAseq batch1
B28_Hipp_RNA

source_name: Hippocampus

value: Hippocampus


title: E13_SkeletalMuscle

description:
E13
208114950100_R06C01


title: IMR32_Prex_24h_R4

description: Library name: IMR32_Prex_24h_R4

value: Prexasertib single low dose


title: IMR32_Prex_Dyngo4a_24h_R4

description: Library name: IMR32_Prex_Dyngo4a_24h_R4


title: M52_DNA_pre

value: F

value: Pre Vacc


title: IMR32_Prex_24h_R3

description: Library name: IMR32_Prex_24h_R3


title: M61_ALVAC_wk12

value: ALVAC group

value: ALVAC


title: LT_A_Ex, Animal B28, Frontal_cortex

description:
RNAseq batch1
B28_FCTX_RNA


title: E29_Colon

description:
E29
208114950100_R04C01

source_name: Colon

value: Colon


title: IMR32_Prex_24h_R2

description: Library name: IMR32_Prex_24h_R2

value: Brain

value: neuroblast

value: WT


title: E32_Colon

description:
E32
208114950100_R05C01


title: LT_A_ctrl, Animal B34, Frontal_cortex

description:
RNAseq batch1
B34_FCTX_RNA


title: DFER_ALVAC_pre

value: DFER

value: M


title: E13_Colon

description:
E13
208114950100_R03C01


title: IMR32_Prex_Dyngo4a_24h_R2

description: Library name: IMR32_Prex_Dyngo4a_24h_R2

value: Prexasertib + dyngo4a combination


title: IMR32_Prex_24h_R1

description: Library name: IMR32_Prex_24h_R1


title: IMR32_Dyngo4a_IC50_24h_R4

description: Library name: IMR32_Dyngo4a_IC50_24h_R4

value: Dyngo4a high dose


title: E29_Hippo

description:
E29
208114950100_R02C01

value: Hippo


title: DFIA_ALVAC_wk36

value: DFIA


title: LT_A_ctrl, Animal B27, Circulating_WBCs

description:
RNAseq batch1
B27_WBC_RNA


title: H304_ALVAC_wk12


title: LT_A_ctrl, Animal B27, Kidney

description:
RNAseq batch1
B27_Kid_RNA

source_name: Kidney

value: Kidney


title: E13_Hippo

description:
E13
208114950100_R01C01


title: LT_A_ctrl, Animal B27, Skeletal_muscle

description:
RNAseq batch1
B27_SkeletalMuscle_RNA


title: H143_DNA_wk36

value: DNA group

value: DNA


title: LT_A_ctrl, Animal B27, Hippocampus

description:
RNAseq batch1
B27_Hipp_RNA

value: Hippocampus


title: IMR32_Dyngo4a_IC50_24h_R2

description: Library name: IMR32_Dyngo4a_IC50_24h_R2


title: LT_A_Ex, Animal B28, Hypothalamus

description:
RNAseq batch1
B28_HTH_RNA

source_name: Hypothalamus

value: Hypothalamus


title: LT_A_ctrl, Animal B27, Hypothalamus

description:
RNAseq batch1
B27_HTH_RNA


title: A47_Hippo

description:
A47
208114950099_R06C02


title: LT_A_ctrl, Animal B27, Frontal_cortex

description:
RNAseq batch1
B27_FCTX_RNA


title: IMR32_Dyngo4a_IC50_24h_R1

description: Library name: IMR32_Dyngo4a_IC50_24h_R1


title: A44_Adipose

description:
A44
208114950099_R04C02

source_name: Adipose

value: Adipose


title: DFGZ_ALVAC.control_wk12

value: DFGZ

value: Controls challenged with ALVAC group

value: ALVAC control


title: IMR32_Dyngo4a_24h_R4

description: Library name: IMR32_Dyngo4a_24h_R4

value: Brain

value: neuroblast

value: Dyngo4a single low dose


title: DEWT_DNA.control_pre

value: DEWT

value: M

value: Controls challenged with DNA group

value: Pre Vacc

value: DNA control


title: LT_A_Ex, Animal B26, Circulating_WBCs

description:
RNAseq batch1
B26_WBC_RNA


title: A46_FCTX

description:
A46
208114950099_R03C02

source_name: FCTX

value: FCTX


title: DFAN_DNA_wk12

source_name: Whole blood

value: DFAN

value: DNA group


title: IMR32_Dyngo4a_IC50_24h_R3

description: Library name: IMR32_Dyngo4a_IC50_24h_R3

value: WT

value: Dyngo4a high dose


title: 01F_ALVAC_pre

value: F

value: ALVAC group

value: ALVAC


title: IMR32_Dyngo4a_24h_R3

description: Library name: IMR32_Dyngo4a_24h_R3


title: IMR32_Dyngo4a_24h_R2

description: Library name: IMR32_Dyngo4a_24h_R2


title: LT_A_Ex, Animal B26, Skeletal_muscle

description:
RNAseq batch1
B26_SkeletalMuscle_RNA


title: A43_FCTX

description:
A43
208114950099_R02C02


title: IMR32_Dyngo4a_24h_R1

description: Library name: IMR32_Dyngo4a_24h_R1


title: A47_FCTX

description:
A47
208114950099_R01C02


title: DEZV_DNA.control_wk36

value: DEZV


title: LT_A_Ex, Animal B26, Hippocampus

description:
RNAseq batch1
B26_Hipp_RNA

value: Hippocampus


title: LT_A_Ex, Animal B26, Kidney

description:
RNAseq batch1
B26_Kid_RNA

value: Kidney


title: A46_Adipose

description:
A46
208114950099_R05C02

value: Adipose


title: A44_WBC

description:
A44
208114950099_R06C01

source_name: WBC

value: WBC


title: IMR32_DMSO_24h_R4

description: Library name: IMR32_DMSO_24h_R4

value: Brain

value: neuroblast

value: DMSO


title: MRP_DNA.control_wk12

value: MRP

value: Controls challenged with DNA group

value: DNA control


title: LT_A_Ex, Animal B26, Hypothalamus

description:
RNAseq batch1
B26_HTH_RNA

value: Hypothalamus


title: A43_WBC

description:
A43
208114950099_R05C01


title: IMR32_DMSO_24h_R3

description: Library name: IMR32_DMSO_24h_R3

value: WT


title: DFCD_DNA_pre

value: DFCD

value: M

value: DNA group

value: Pre Vacc

value: DNA


title: LT_A_Ex, Animal B26, Frontal_cortex

description:
RNAseq batch1
B26_FCTX_RNA


title: IMR32_DMSO_24h_R2

description: Library name: IMR32_DMSO_24h_R2


title: E36_Hippo

description:
E36
208114950099_R04C01

value: Hippo


title: DFAP_ALVAC_pre

value: DFAP

value: ALVAC group

value: ALVAC


title: E28_Adipose

description:
E28
208114950099_R03C01

value: Adipose


title: MR32_DMSO_24h_R1

description: Library name: MR32_DMSO_24h_R1

value: Brain

value: neuroblast


title: LT_A_Ex, Animal B25, Circulating_WBCs

description:
RNAseq batch1
B25_WBC_RNA


title: DF49_ALVAC_wk36


title: LT_A_Ex, Animal B25, Skeletal_muscle

description:
RNAseq batch1
B25_SkeletalMuscle_RNA


title: iNeuron, shTDP-43, day 7, 3'end-seq, rep 3

city: Stanford

first: Yi

last: Zeng

address: 300 Pasteur Drive

institute: Stanford University

data_processing:
library strategy: 3'end-seq
For RNA-seq data, adaptors in FASTQ files were removed using fastp. For differential gene expression analysis, the adapter trimmed FASTQ files were analyzed using Salmon and DESeq2. The normalized gene counts were calculated  in DESeq2 and exported. For splicing analysis, the adapter trimmed FASTQ files were first mapped to human geneom using STAR following the ENCODE recommended settings. The unique-mapping, properly paired reads were then used for splicing analysis using leafcutter. Thre resulting clusters and introns that showed signficant changes upon TDP-43 knockdown were exported. For alternative polyadenylation analysis, the unique-mapping, properly paired reads were then used for APA detection by either APAlyzer and then differential analysis by DEXseq. The APA results were exported.
For 3' end-seq, FASTQ files were adapter-trimmed, and quality filtered using bbduk. The filtered reads were mapped to human genome (hg38) using STAR and then extracted for unique-mapping, properly paired reads using Samtools. If a read was mapped to a region that is immediately upstream of six consecutive As or of a 10-bp region with at least 60% of As, it was considered as a mis-primed read and removed. The resulting filtered reads were analyzed using a modified version of LAPA that used the default setting, except requiring a replication rate cutoff at 0.75 and can identify polyA site-containing reads mapped to the reverse strand. Signficant APA events and cryptic polyadenylation events were exported.
Assembly: hg38
Supplementary files format and content: D7-scr-vs-kd-gene-normalized-counts.csv: comma-delimited text file includes normalized gene counts for each sample.
Supplementary files format and content: D7-scr-vs-kd-leafcutter-sig-clusters.tsv: tab-deliminted text file includes clusters that show significant splicing changes upon TDP-43 knockdown.
Supplementary files format and content: D7-scr-vs-kd-leafcutter-sig-introns.tsv: tab-deliminted text file includes introns that show significant splicing changes upon TDP-43 knockdown.
Supplementary files format and content: D7-scr-vs-kd-sig-APA-RNA-seq.csv: comma-deliminted text file includes 3' UTRs that show significant alternative polyadenylation changes upon TDP-43 knockdown.
Supplementary files format and content: D7-scr-vs-kd-sig-APA-changes-3end-seq.csv: comma-deliminted text file includes genes that showed significant alternative polyadenylation changes upon TDP-43 knockdown from 3' end-seq experiment.
Supplementary files format and content: cryptic-polyadenylatin-3end-seq.csv: comma-deliminted text file includes cryptic polyadenylatione events upon TDP-43 knockdown from 3' end-seq experiment.

growth_protocol: Human embryonic stem cells are differentiated to cortical neurons by inducing the over-expression of NGN2

extract_protocol:
After 7-day knockdown, total RNA was extracted using trizol and further treated with Turbo DNAse to remove residual genomic DNA
RNA-seq libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara 634411), according to the manufacturer’s instructions; 3' end-seq libraries were constructed using Quantseq REV kit (Lexogen), according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with either scrambled shRNA or TDP-43 shRNA for 7 days

value: Human embryonic stem cells

value: TDP-43 knockdown

value: NGN2-mediated differentiation


title: LT_A_Ex, Animal B25, Kidney

description:
RNAseq batch1
B25_Kid_RNA

value: Kidney


title: E10_Adipose

description:
E10
208114950099_R02C01


title: E10_FCTX

description:
E10
208114950098_R06C02

value: FCTX


title: iNeuron, shTDP-43, day 7, 3'end-seq, rep 2


title: MRR_ALVAC_wk12

value: MRR

value: F


title: LT_A_Ex, Animal B25, Hippocampus

description:
RNAseq batch1
B25_Hipp_RNA

value: Hippocampus


title: E28_FCTX

description:
E28
208114950099_R01C01


title: MRR_ALVAC_wk36


title: iNeuron, shControl, day 7, 3'end-seq, rep 3

value: WT


title: DFGC_DNA_wk36

value: DFGC

value: M

value: DNA group

value: DNA


title: iNeuron, shTDP-43, day 7, 3'end-seq, rep 1


title: LT_A_Ex, Animal B25, Hypothalamus

description:
RNAseq batch1
B25_HTH_RNA

value: Hypothalamus


title: E36_FCTX

description:
E36
208114950098_R05C02


title: LT_A_Ex, Animal B25, Frontal_cortex

description:
RNAseq batch1
B25_FCTX_RNA


title: DEVV_DNA_wk12

value: DEVV


title: E28_WBC

description:
E28
208114950098_R04C02

value: WBC


title: iNeuron, shControl, day 7, 3'end-seq, rep 2


title: M36_DNA_wk36


title: E10_WBC

description:
E10
208114950098_R03C02


title: iNeuron, shControl, day 7, 3'end-seq, rep 1


title: LT_A_ctrl, Animal B24, Circulating_WBCs

description:
RNAseq batch1
B24_WBC_RNA


title: H143_DNA_pre

value: Pre Vacc


title: E34_Hippo

description:
E34
208114950098_R02C02

value: Hippo


title: iNeuron, shTDP-43, day 7, RNA-seq, rep 3

data_processing:
For RNA-seq data, adaptors in FASTQ files were removed using fastp. For differential gene expression analysis, the adapter trimmed FASTQ files were analyzed using Salmon and DESeq2. The normalized gene counts were calculated  in DESeq2 and exported. For splicing analysis, the adapter trimmed FASTQ files were first mapped to human geneom using STAR following the ENCODE recommended settings. The unique-mapping, properly paired reads were then used for splicing analysis using leafcutter. Thre resulting clusters and introns that showed signficant changes upon TDP-43 knockdown were exported. For alternative polyadenylation analysis, the unique-mapping, properly paired reads were then used for APA detection by either APAlyzer and then differential analysis by DEXseq. The APA results were exported.
For 3' end-seq, FASTQ files were adapter-trimmed, and quality filtered using bbduk. The filtered reads were mapped to human genome (hg38) using STAR and then extracted for unique-mapping, properly paired reads using Samtools. If a read was mapped to a region that is immediately upstream of six consecutive As or of a 10-bp region with at least 60% of As, it was considered as a mis-primed read and removed. The resulting filtered reads were analyzed using a modified version of LAPA that used the default setting, except requiring a replication rate cutoff at 0.75 and can identify polyA site-containing reads mapped to the reverse strand. Signficant APA events and cryptic polyadenylation events were exported.
Assembly: hg38
Supplementary files format and content: D7-scr-vs-kd-gene-normalized-counts.csv: comma-delimited text file includes normalized gene counts for each sample.
Supplementary files format and content: D7-scr-vs-kd-leafcutter-sig-clusters.tsv: tab-deliminted text file includes clusters that show significant splicing changes upon TDP-43 knockdown.
Supplementary files format and content: D7-scr-vs-kd-leafcutter-sig-introns.tsv: tab-deliminted text file includes introns that show significant splicing changes upon TDP-43 knockdown.
Supplementary files format and content: D7-scr-vs-kd-sig-APA-RNA-seq.csv: comma-deliminted text file includes 3' UTRs that show significant alternative polyadenylation changes upon TDP-43 knockdown.
Supplementary files format and content: D7-scr-vs-kd-sig-APA-changes-3end-seq.csv: comma-deliminted text file includes genes that showed significant alternative polyadenylation changes upon TDP-43 knockdown from 3' end-seq experiment.
Supplementary files format and content: cryptic-polyadenylatin-3end-seq.csv: comma-deliminted text file includes cryptic polyadenylatione events upon TDP-43 knockdown from 3' end-seq experiment.

value: Human embryonic stem cells

value: TDP-43 knockdown


title: DFFM_ALVAC_wk12

value: DFFM

value: ALVAC group

value: ALVAC


title: H306_ALVAC.control_wk12

value: F

value: Controls challenged with ALVAC group

value: ALVAC control


title: E33_Adipose

description:
E33
208114950098_R01C02

value: Adipose


title: iNeuron, shTDP-43, day 7, RNA-seq, rep 2

value: NGN2-mediated differentiation


title: LT_A_ctrl, Animal B24, Kidney

description:
RNAseq batch1
B24_Kid_RNA

value: Kidney


title: E15_Adipose

description:
E15
208114950098_R06C01


title: LT_A_ctrl, Animal B24, Hypothalamus

description:
RNAseq batch1
B24_HTH_RNA


title: E33_FCTX

description:
E33
208114950098_R05C01

value: FCTX


title: iNeuron, shTDP-43, day 7, RNA-seq, rep 1


title: primary endometriotic stromal cells, TCF21, ChIP

city: Beijing

first: Jie

address: 8 Xishiku Rd., Xicheng District

institute: Peking University First Hospital

description: Library name: primary endometriotic stromal cells_TCF21_ChIP

data_processing:
Bench top CUT&Tag V.3
Assembly: hg38
Supplementary files format and content: bigWig, narrowpeak
Library strategy: CUT&Tag

source_name: endometriotic lesions

extract_protocol:
CUT & Tag library was prepared by NovoNGS® CUT&Tag High‐Sensitivity Kit (Novoprotein). In brief, approximately 1 × 105 endometriotic stromal cells were isolated and incubated with NovoNGS® ConA Beads. Subsequently, antibodies and ChiTag transposons were sequentially attached to the chromatin. Following this step, DNA fragments were obtained, amplified, and purified.
Genomic fragments with adapters at both ends were enriched by PCR and sequenced by Novogene Bioinformatics Technology on the HiSeq 2500 platform (Illumina). Trimmed reads were aligned to hg38 using Bowtie2 and peaks were called by MACS2. Peak distribution at genomic regions of interest was depicted using the Integrative Genomics Viewer (IGV).

value: endometriotic lesions

value: primary endometriotic stromal cells

value: Human endometriotic stromal cell

value: anti-TCF21 antibody (Santa Cruz Biotechnology; sc-377225)


title: LT_A_ctrl, Animal B15, Circulating_WBCs

description:
RNAseq batch1
B15_WBC_RNA


title: iNeuron, shControl, day 7, RNA-seq, rep 1

value: WT


title: E15_FCTX

description:
E15
208114950098_R04C01


title: iNeuron, shControl, day 7, RNA-seq, rep 2

value: Human embryonic stem cells


title: OMA_4

description:
Library name: OMA_4
OSA_REN

data_processing:
CLC Genomics Workbench 22.0.1
Assembly: hg38
Supplementary files format and content: FPKM for each sample

source_name: ectopic endometrium

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) , 1μg of total RNA was used for the construction of RNA libraries
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

value: ectopic endometrium


title: iNeuron, shControl, day 7, RNA-seq, rep 3


title: LT_A_ctrl, Animal B24, Skeletal_muscle

description:
RNAseq batch1
B24_SkeletalMuscle_RNA


title: E33_WBC

description:
E33
208114950098_R02C01

value: WBC


title: LT_A_ctrl, Animal B15, Skeletal_muscle

description:
RNAseq batch1
B15_SkeletalMuscle_RNA


title: kidney, db/db_rep9

city: Amsterdam

first: Alessandra

last: Tammaro

state: AZ

address: Meibergdreef 05

department: Department of pathology

country: Netherlands

institute: Amsterdam University Medical Center

description: Library name: K76_db/db_rep9

data_processing:
Sequencing reads were trimmed with BBDuk (BBTools version 36.84, Bushnell B., sourceforge.net/projects/bbmap/).
Mapping to the mouse genome (built GRCh38.101) was performed with RNA STAR, version 2.7.3a, using default parameters.
Gene count was performed with HTSeq, version 2.16.2.
Assembly: mouse genome (built GRCh38.101)
Supplementary files format and content: htseq counts

source_name: kidney

extract_protocol:
Total RNA was extracted from cells seeded in 6-well plates using Agencourt RNAdvance Tissue kit (Beckman Coulter Life sciences #A32646).
100 ng was used to generate libraries using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen #193.384).
QuantSeq

value: kidney

value: db/m


title: LT_A_ctrl, Animal B15, Kidney

description:
RNAseq batch1
B15_Kid_RNA


title: kidney, db/db_rep8

description: Library name: K68_db/db_rep8


title: EM_4

description:
Library name: EM_4
EM_REN

source_name: eutopic endometrium

value: eutopic endometrium


title: E34_FCTX

description:
E34
208114950098_R03C01


title: E15_WBC

description:
E15
208114950098_R01C01


title: LT_A_ctrl, Animal B24, Hippocampus

description:
RNAseq batch1
B24_Hipp_RNA

value: Hippocampus


title: OMA_3

description:
Library name: OMA_3
OSA_LI


title: kidney, db/db_rep7

description: Library name: K54_db/db_rep7