title: CS_M_50_biol rep1

city: Waltham

first: Sebastian

last: Kadener

state: Massachusetts

address: 415 South Street

institute: Brandeis University

data_processing:
Data was aligned using STAR to Drosophila melanogaster genome version dm6.
Counting number of reads for each gene was done using featureCounts (Liao et al., 2014).
circRNAs were detected by searching unaligned reads for head-to-tail splice junctions as previously described (Memczak et al., 2013).
Assembly: dm6
Supplementary files format and content: Excel sheet with normalized counts of linear and circular RNA for each sample.

source_name: head

growth_protocol: Flies were grown at 25C in 12:12 Light:dark.

extract_protocol:
Trizol RNA extraction (SIGMA) followed by DNase I (NEB) treatment following manufacturer's instructions.
1 ug of RNA was ribodepleted using Hybridase thermostable RNaseH (Epicentre, H39500) and total libraries were prepared using NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (PerkinElmer) as recommended by the manufacturer.

treatment_protocol: Flies were flipped every 2-3 days until they reached the desired age and were flash frozen.

value: head

value: CS

value: WT

value: male

value: 50 days old


title: WCS19_E_3

status: Public on Mar 03 2025

type: SRA

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

library_source: transcriptomic

data_processing:
The sequenced reads generated from RNA-seq were mapped onto the reference genome (GCA_000184185.1) using bowtie2. The mapped information was converted as bam file format, and the number of mapped reads at each gene was counted using htseq-count pipeline. Differentially expressed genes were calculated with DESeq2. As a normalized count metric, transcripts per million (TPM) was manually calculated.
Assembly: GCA_000184185.1
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

molecule: total RNA

organism: Escherichia coli W

source_name: bacterial cell

growth_protocol: For itaconic acid production, strains were grown at a modified M9 acetate medium with 0.5 g/L MgSO4·7H2O, 2 g/L NH4Cl, 1 g/L NaCl, 2 g/L L-glutamic acid, 2 g/L yeast extract, 100 mM potassium phosphate buffer for pH balancing for the value of 7, and 10 g/L of neutralized acetate (adjusted to pH 7 by adding 10 M NaOH)

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer's instructions. RNA concentration was quantified using a NanoDrop OneC spectrophotometer (Thermo Scientific). The quality of the isolated RNA was checked by running 1% agarose gel electrophoresis.
One microgram of the RNA from each sample was used for rRNA depletion with riboPOOL (siTOOLs Biotech) and Dynabeads MyOne Streptavidin C1 (Invitrogen), followed by purification using RNA Clean & Concentrator Kit (Zymo Research) according to the manufacturer's instructions. The suitable RNA samples were then used to construct paired-end, strand-specific RNA-seq libraries using KAPA RNA Hyper Prep kit (Kapa Biosystems) with the modification of shortened fragmentation of 2 minutes at 85℃ to include sRNAs in the library. The concentration of the final library was measured with Qubit 4 fluorometer (Thermo Scientific) and the size distribution was checked with Agilent 2100 Bioanalyzer (Agilent). The library was sequenced on NextSeq 550 (Illumina) platform with NextSeq 500/550 High Output Kit v2.5 (Illumina) in accordance with the manufacturer's instructions. All RNA-seq experiments were performed in biological triplicate.

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

tag: strain

tag: genotype

value: ale

tag: phase

value: mid-exponential phase

tag: cell type

value: bacterial cell


title: CS_M_40_biol rep3

country: USA

organism: Drosophila melanogaster

tag: tissue

tag: Sex

tag: age

value: 40 days old


title: Muscle, exercise, 22

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference with STARv2.7.9a
Alternative splicing analysis via Whippetv1.6.2 and rMATSv4.1.1
Assembly: mm10
Supplementary files format and content: Excel file containing the Alternative splicing events

organism: Mus musculus

source_name: skeletal muscle

extract_protocol:
total RNA was extracted using the miRNAeasy Mini Kit (Qiagen, Germany) as per the manufacturer's protocol, with additional DNase treatment
done by BGI (Yantian District, Shenzhen, China)

value: skeletal muscle

value: Male

tag: treatment

value: Exercise

tag: intervention group

value: exercise(EX)


title: WCS19_E_2


title: Sample 36_IL1-R1 KO 28d 162ug

type: RNA

city: Ottawa

first: Sabina

last: Halappanavar

state: Ottawa

address: 251 Sir Frederick Banting Dr.

country: Canada

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Lung

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Five-to-seven week old female wild type C57BL/6 mice (WT) and C57BL/6 mice deficient in IL1-R1 (IL1-R1 KO)  (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and heart were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Wild type (WT) C57BL/6 and IL1-R1 KO mice were exposed to Mitsui-7 (multiwalled carbon nanotubes (MWCNT)) at a dose of 162 µg/mouse by intratracheal administration in a 50 µl suspension   Tissues were collected 1 and 28 days post-instillation.

value: lung

tag: gender

value: Female

value: IL1-R1 deficient C57BL/6 mice

tag: dose

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines

tag: sample type

value: reference


title: WCS19_E_1


title: Muscle, exercise, 21


title: CS_M_40_biol rep2

value: head

value: CS


title: WCS6_S_3

value: stationary phase


title: Adipose tissue, intermittent fasting, 24

source_name: White adipose tissue

value: White adipose tissue

value: NZO/HIBomDife

value: Intermittent Fasting

value: Ad libitum(AL)


title: Sample 33_IL1-R1 KO 1d Control


title: Muscle, exercise, 20


title: Sample 34_IL1-R1 KO 1d 162ug


title: CS_M_50_biol rep2

value: WT

value: male

value: 50 days old


title: CS_M_40_biol rep1

value: 40 days old


title: WCS6_S_2

value: ale

value: bacterial cell


title: Muscle, exercise, 19

value: skeletal muscle

value: Male

value: Exercise

value: exercise(EX)


title: CS_M_30_biol rep3

value: head

value: 30 days old


title: Muscle, exercise, 18

value: sedentary(SED)


title: WCS6_S_1

value: stationary phase


title: Sample 4_ 28d, STAT6KO, 162ug

growth_protocol: Five-to-seven week old female wild type C57BL/6 mice (WT) and C57BL/6 mice deficient in  STAT6 (STAT6 KO) (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

treatment_protocol: Wild type (WT) C57BL/6 and STAT6 KO mice were exposed to Mitsui-7 (multiwalled carbon nanotubes (MWCNT)) at a dose of 162 µg/mouse by intratracheal administration in a 50 µl suspension   Tissues were collected 1 and 28 days post-instillation.

value: lung

value: Female

value: STAT6 deficient C57BL/6 mice

value: 11 mouse cell lines

value: reference


title: Sample 29_WT 1d Control

value: wild type C57BL/6 mice


title: Sample 32_IL1-R1 KO 28d Control

value: IL1-R1 deficient C57BL/6 mice


title: Sample 31_WT 1d 162ug


title: CS_M_30_biol rep2

value: CS

value: WT

value: male


title: Sample 28_IL1-R1 KO 1d Control


title: Muscle, exercise, 17

value: skeletal muscle

value: Male


title: Sample 30_WT 28d 162ug


title: CS_M_30_biol rep1


title: WCS6_T_3

value: ale

value: transition phase

value: bacterial cell


title: Muscle, exercise, 16

value: Exercise

value: sedentary(SED)


title: WCS6_T_2


title: WCS19_S_2

value: stationary phase


title: Sample 27_ IL1-R1 KO 28d 162ug

value: lung

value: Female


title: WCS6_T_1


title: CS_M_20_biol rep1

value: head

value: 20 days old


title: WCS6_E_3

value: mid-exponential phase


title: Muscle, exercise, 14


title: CS_M_10_biol rep3

value: 10 days old


title: Muscle, intermittent fasting, 13

value: NZO/HIBomDife

value: Intermittent Fasting

value: caloric restriction(CR)


title: WCS6_E_2


title: Sample 26_WT 28d Control

value: wild type C57BL/6 mice

value: 11 mouse cell lines

value: reference


title: Muscle, intermittent fasting, 12

value: skeletal muscle

value: Male


title: CS_M_10_biol rep1

value: CS

value: WT

value: male


title: CS_M_20_biol rep2


title: Muscle, exercise, 15

value: Exercise

value: sedentary(SED)


title: WCS6_E_1

value: ale

value: bacterial cell


title: Muscle, intermittent fasting, 11


title: Sample 25_IL1-R1 KO 1d 162ug

value: lung

value: Female

value: IL1-R1 deficient C57BL/6 mice


title: CS_M_0_biol rep2

value: head

value: mated for 3 days


title: CS_M_0_biol rep1


title: Sample 23_WT 28d Control

value: wild type C57BL/6 mice


title: Sample 24_WT 1d Control

value: 11 mouse cell lines


title: Sample 22_WT 1d 162ug

value: reference


title: CS_M_0_biol rep3


title: WCS0_S_3

value: parental

value: stationary phase


title: WCS0_S_2


title: WCS0_S_1


title: Muscle, intermittent fasting, 9

value: skeletal muscle

value: NZO/HIBomDife

value: Male

value: Intermittent Fasting

value: intermittent fasting(IF)


title: Muscle, intermittent fasting, 8


title: CS_F_50_biol rep3

value: CS

value: WT

value: female

value: 50 days old


title: WCS0_T_3

value: transition phase

value: bacterial cell


title: CS_F_50_biol rep2

value: head


title: Muscle, intermittent fasting, 7


title: Muscle, intermittent fasting, 10


title: WCS0_T_2


title: CS_F_50_biol rep1


title: Muscle, intermittent fasting, 6


title: CS_F_40_biol rep3

value: 40 days old


title: Sample 18_IL1-R1 KO 28d 162ug

value: lung

value: Female

value: IL1-R1 deficient C57BL/6 mice

value: 11 mouse cell lines


title: Muscle, intermittent fasting, 5

value: skeletal muscle

value: Ad libitum(AL)


title: Sample 19_WT 28d 162ug

value: wild type C57BL/6 mice

value: reference


title: Sample 20_IL1-R1 KO 1d 162ug


title: WCS0_E_3

value: parental

value: mid-exponential phase


title: CS_F_40_biol rep2

value: CS

value: WT


title: Sample 21_IL1-R1 KO 28d Control


title: WCS0_E_2


title: Muscle, intermittent fasting, 3

value: NZO/HIBomDife

value: Male

value: Intermittent Fasting


title: Muscle, intermittent fasting, 4


title: WCS0_E_1

value: bacterial cell


title: Sample 15_WT 1d 162ug


title: CS_F_40_biol rep1

value: head

value: female

value: 40 days old


title: CS_F_30_biol rep2

value: 30 days old


title: CS_F_30_biol rep3


title: Dorsal skin, WT corn snake 3, stage 7 (embryonic day 20)

city: Geneva

first: Athanasia

last: Tzika

address: Quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description:
D_Mot_WT3
raw_counts.tsv

data_processing:
Sequence reads were mapped to the GCF_029531705.1 genome assembly using STAR v2.7.10b with default parameters for paired-end libraries.
Gene expression quantification was performed using the featureCounts function implemented in the Subread package (v2.0.6) counting uniquely mapped paired-end reads.
Assembly: GCF_029531705.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

organism: Pantherophis guttatus

source_name: Dorsal skin

extract_protocol:
Total RNA was extracted using the Direct-zol RNA MiniPrep (Zymo Research, R2050)
Library was constucted using TruSeq Stranded mRNA kit

value: Dorsal skin

tag: time point

value: stage 7 (embryonic day 20)


title: Muscle, intermittent fasting, 2

value: skeletal muscle

value: Ad libitum(AL)


title: Dorsal skin, WT corn snake 2, stage 7 (embryonic day 20)

description:
D_Mot_WT2
raw_counts.tsv


title: Muscle, intermittent fasting, 1


title: CS_F_30_biol rep1


title: RAW264.7 cell, medium+10nM Dox, rep5

city: Shanghai

first: Heng

last: Wang

state: Shanghai

address: No.1630, Dongfang Road, Pudong New District, Shanghai, China.

department: Cardiovascular Surgery

country: China

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

description: Library name: Doxorubicin_5

data_processing:
Data were processed by StringTie2
Assembly: GRCm39
Supplementary files format and content: The file include FPKM values for all samples

source_name: Tumor

growth_protocol: RAW264.7 cells were cultured by minimum essential medium (Shanghai Epizyme Biomedical Technology, CB009), 10%(v/v) fetal bovine serum (Nobimpex Biotechnology, B119-500), 1× penicillin-streptomycin (Yeasen Biotechnology (Shanghai), 60162ES76) under 37℃, 5%(v/v) CO2 condition.

extract_protocol:
cells in each well were lyzed by 0.5ml TRNzol Universal buffer (TIANGEN Biochemical Technology (Beijing), DP424) on a slowly swinging rocker at 4℃ for 15min, and then collected into a cryogenic storage tube and stored at -80℃. The RNA was extracted by chloroform (Sigma-Aldrich, CX1060)
The mRNA in each sample was enriched by Oligo (dT) magnetic beads and fragmented by the metal ion solution. Then reverse transcription was done using the M-MuLV system and random oligonucleotide primers, and the sticky ends of end-repaired, double-strand cDNA with poly-A tail was catalyzed by T4 DNA ligase with short adapters.AMPure XP beads were used for post-ligation purification, followed by size selection of cDNA fragments around 300-350bp. Polymerase chain reaction (PCR) was conducted to incorporate sample indices, and the PCR products were purified with AMPure XP beads to obtain the final library. The library was quantified, diluted, and analyzed for fragment distribution with the Agilent 2100 DNA 1000 kit. Quality control was confirmed, and qRT-PCR was used for precise quantification of the library's effective concentration to ensure quality.

treatment_protocol: RAW264.7 cells were treated by medium and medium plus 0.001%(v/v) 100mM doxorubicin-dimethyl sulfoxide (DMSO) for 24h.

value: Tumor

tag: cell line

value: RAW264.7 cells

value: Macrophage

value: Medium+Doxorubicin


title: Dorsal skin, WT corn snake 1, stage 7 (embryonic day 20)

description:
D_Mot_WT1
raw_counts.tsv

value: WT


title: Dorsal skin, Homozygous Motley corn snake 4, stage 7 (embryonic day 20)

description:
D_Mot_Hom4
raw_counts.tsv

value: Homozygous Motley


title: CS_F_20_biol rep3

value: CS

value: 20 days old


title: RAW264.7 cell, medium+10nM Dox, rep4

description: Library name: Doxorubicin_4


title: Sample 17_WT 28d Control

value: lung

value: Female

value: wild type C57BL/6 mice

value: 11 mouse cell lines

value: reference


title: Sample 3_1d, STAT6 KO, Control

value: STAT6 deficient C57BL/6 mice


title: Sample 14_WT 28d 162ug


title: CS_F_20_biol rep2

value: head

value: female


title: Sample 13_WT 1d Control


title: Sample 12_WT 28d 162ug


title: RAW264.7 cell, medium+10nM Dox, rep3

description: Library name: Doxorubicin_3


title: CS_F_20_biol rep1


title: RAW264.7 cell, medium+10nM Dox, rep2

description: Library name: Doxorubicin_2


title: Dorsal skin, Homozygous Motley corn snake 2, stage 7 (embryonic day 20)

description:
D_Mot_Hom2
raw_counts.tsv

value: Dorsal skin

value: stage 7 (embryonic day 20)


title: Sample 16_IL1-R1 KO 1d 162ug

value: IL1-R1 deficient C57BL/6 mice


title: RAW264.7 cell, medium+10nM Dox, rep1

description: Library name: Doxorubicin_1

value: Tumor

value: RAW264.7 cells

value: Macrophage


title: CS_F_10_biol rep3

value: WT

value: 10 days old


title: Dorsal skin, Homozygous Motley corn snake 1, stage 7 (embryonic day 20)

description:
D_Mot_Hom1
raw_counts.tsv

value: Homozygous Motley


title: Sample 9_IL1-R1 KO 28d 162ug

value: lung


title: CS_F_10_biol rep2

value: CS


title: Sample 11_WT 1d Control

value: Female

value: wild type C57BL/6 mice


title: Sample 8_IL1-R1 KO 28d Control

value: 11 mouse cell lines

value: reference


title: RAW264.7 cell, medium, 24h, rep5

description: Library name: Control_5

value: Medium


title: WCS0_T_1

value: parental

value: transition phase

value: bacterial cell


title: Sample 10_WT 1d 162ug


title: CS_F_10_biol rep1

value: head

value: female


title: Dorsal skin, Homozygous Motley corn snake 3, stage 7 (embryonic day 20)

description:
D_Mot_Hom3
raw_counts.tsv

value: Dorsal skin

value: stage 7 (embryonic day 20)


title: F.excelsior 2451S new genome using ONT 1

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: Centre for Novel Agricultural Products, University of York

description:
2020015_AH_Ash_PromethION.fast5.tar.gz
Flow cell FLO-PRO002
PromethION R9.4.1

library_source: genomic

data_processing:
Base calling with guppy
Assembly with canu 2.1.1
Phased with purge haplotigs and polished with Pilon using Illumina data (ERR1399574)
Nanopolish v.0.13.2
calculate_methylation_frequency.py
Assembly: Fraxinus excelsior 2451S ONT
Supplementary files format and content: Methylation called using nanopolish
Supplementary files format and content: Methylation frequency calculated with the script calculate_methylation_frequency.py

molecule: genomic DNA

organism: Fraxinus excelsior

source_name: Leaves

extract_protocol:
gDNA extracted from high molecular weight gDNA extraction from plant leaves protocol, Oxford Nanopore Technologies [ONT], which utilised Carlson buffer and further purification using QIAGEN genomic-tip, see preprint Vaillancourt and Buell (2019) for details
the SQK-LSK109 ligation sequencing kit
Single-run with PromethION R9.4.1 (FLO-PRO002) flow cells

value: Leaves


title: Sample 7_IL1-R1 KO 1d Control

value: IL1-R1 deficient C57BL/6 mice


title: F.excelsior 2451S new genome using ONT 2

description:
20200115_AH_Ash.PromethION.pass.fastq
Flow cell FLO-PRO002
PromethION R9.4.1


title: RAW264.7 cell, medium, 24h, rep4

description: Library name: Control_4

value: Tumor

value: RAW264.7 cells

value: Macrophage

value: WT


title: CS_F_0_biol rep3

value: CS

value: mated for 3 days


title: Sample 5_WT 1d 162ug

value: lung

value: Female

value: wild type C57BL/6 mice

value: 11 mouse cell lines

value: reference


title: Sample 6_IL1-R1 KO 28d Control


title: Sample 4_WT 28d 162ug


title: DNASH35-susceptible tree

description:
SQK-LSK109 ligation sequencing kit
Flow cell FLO-PRO002

data_processing:
Base calling with guppy
Nanopolish v.0.13.2
calculate_methylation_frequency.py
Assembly: Fraxinus excelsior 2451S ONT
Supplementary files format and content: Methylation called using nanopolish
Supplementary files format and content: Methylation frequency calculated with the script calculate_methylation_frequency.py

extract_protocol:
DNA was extracted using the method of Workman et al., (Workman et al., 2018) from a pair of Danish trees previously described in Harper et al. (Harper et al., 2016): association panel tree Ash66, and prediction panel tree DNASH35, which had ash dieback disease damage scores of 0 and 75% respectively.
The libraries were prepared using the SQK-LSK109 ligation sequencing kit and run with PromethION R9.4.1 (FLO-PRO002) flow cells

value: DNASH35-susceptible tree


title: CS_F_0_biol rep2

value: head

value: female


title: RAW264.7 cell, medium, 24h, rep1

description: Library name: Control_1

value: Medium


title: Ash66-tolerant tree

value: Leaves

value: Ash66-tolerant tree


title: LE3_1

status: Public on Mar 02 2025

city: Hsinchu

first: Ling-ya

last: Huang

state: Taiwan

address: 1001 University Road

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
hg19
Genome_build: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse melanoma

growth_protocol: Female C57BL/6J mice (4–6 weeks of age) were obtained from the National Laboratory Animal Center (Taipei, Taiwan), and all animal studies were approved and performed in accordance with the standard procedures established by the Institutional Animal Care and Use Committee.

extract_protocol:
Melanoma tumor were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female C57BL/6J mice (n=10) were subcutaneously implanted with 1×104 B16F10 cells in 100 μl of PBS. Three days after implantation, the mice bearing B16F10 tumors were treated with LPPC-DOX (containing 0.5 mg/kg DOX), LPPC-CpG (containing 0.05 mg/kg CpG), LPPC-DOX-CpG (containing 0.5 mg/kg DOX and 0.05 mg/kg CpG) or vehicle by skin application every day. Tumor size was measured with a caliper, and tumor volume was calculated as L × H × W. The mice were sacrificed when the tumor size exceeded 2000 mm3

tag: host strain

value: LPPC

tag: injected cell line


title: LDE4_1

value: LPPC, DOX


title: P01_1

value: PBS


title: LDCE6_1

value: LPPC, DOX, CpG


title: LDCE3_1


title: RAW264.7 cell, medium, 24h, rep3

description: Library name: Control_3

value: Tumor

value: RAW264.7 cells

value: Macrophage

value: WT


title: Sample 3_WT 28d Control

value: lung

value: Female

value: wild type C57BL/6 mice


title: LD02_1


title: LDC06_1


title: LD03_1


title: P02_1


title: LCE5_1

value: LPPC, CpG


title: LCE4_1


title: CS_F_0_biol rep1

value: head

value: CS

value: mated for 3 days


title: L06_1


title: P03_1


title: RAW264.7 cell, medium, 24h, rep2

description: Library name: Control_2

value: Medium


title: L05_1


title: HiC, H9 cell line, with VEGF-A 24hr, rep1

city: Daejeon

first: Gyeongsik

last: Park

state: Daejeon

address: 291 Daehak-ro, Yuseong-gu

department: Biology

institute: KAIST

data_processing:
The sequencing output from Hi-C libraries were mapped to the reference genome (hg19) using BWA-mem (‘–M’ option).
In-house scripts were used to remove low quality reads (MAPQ < 10), the reads that span ligation sites, chimeric reads, and self-interacting reads (two fragments located within 5kb).
The chimeric reads were removed since they are by-products of proximity ligation during Hi-C experiments, and cannot be properly processed by paired-end BWA-mem command.
The read-pairs were merged together as paired-end aligned BAM files, and PCR duplicates were removed with Picard (v2.6.0).
Assembly: hg19
Supplementary files format and content: hic file of an each replication

organism: Homo sapiens

extract_protocol:
Cells were harvested and crosslinked in 1% formaldehyde for 10 min at room temperature. Crosslinked cells were lysed with 10nM Tris-HCl (pH8.0), 10mM NaCl, and 0.2% IGEPAL CA630 (Sigma-Aldrich, 18896), and digested with 100U MboI (NEB, R0147). Digested fragments were labelled with biotin-14-dCTP (Invitrogen, 19518018) and proximally ligated with T4 DNA Ligase (NEB, M0202), followed by reverse-crosslinking with 2 ug/uL proteinase K (NEB, P8102), 1% SDS, and 500mM NaCl overnight at 68°C. The DNA fragments were purified with AMPure XP beads (Beckman Coulter, A63880), and subjected to sonication (Covaris, S220). The ligated DNA fragments were pulled down with Dynabeads MyOne streptavidin T1 beads (Invitrogen, 65602) with thorough washing.
Hi-C libraries were prepared manually by performing DNA end repair, removal of un-ligated ends, adenosine addition at 3’ end (NEB, M0212), ligation of Illumina indexed adapters (NEB, M2200), and PCR amplification (Thermo Fisher Scientific, F549). The number of cycles for PCR amplification was determined based on KAPA library quantification kit (KAPA, KK4854).

value: human embryonic stem cells

value: endothelial differentiation


title: HiC, H9 cell line, with VEGF-A 24hr, rep2


title: LC02_1


title: 3234, chronic liver disease, Non-B Non-C

city: Hiroshima-shi

first: Hikaru

last: Nakahara

address: kasumi 1-2-3, minami-ku

country: Japan

institute: Hiroshima University

data_processing:
Sequencing reads were pre-processed using fastp v0.20.
RSEM was used for mapping and quantification to the human genome GRCh38.p13. STAR was selected as the parameter for mapping.
Assembly: GRCh38
Supplementary files format and content: txt file includes raw counts for each sample
Supplementary files format and content: txt file includes transcripts per million (TPM) value for each sample

source_name: liver

extract_protocol:
Total RNA was extracted from Fresh Frozen liver tissue according to the protocol using QIAGEN's RNeasy Kits. Total RNA was subjected to DNAse treatment with Zymo Research's RNA Clean & Concentrator-5 with DNase I, and 200 ng was used for library construction.
The MGIEasy RNA Directional Library Prep Set and MGISP 100 were used to create DNB. Adapters from the MGIEasy DNA Adapters 96 (Plate) Kit were also used.

value: liver

value: chronic liver disease


title: HiC, H9 cell line, with VEGF-A 4hr, rep2


title: HiC, H9 cell line, with VEGF-A 4hr, rep1


title: 5221, chronic liver disease, Non-B Non-C


title: Sample 1_IL1-R1 KO 28d 162ug

value: IL1-R1 deficient C57BL/6 mice

value: 11 mouse cell lines

value: reference


title: 3112, chronic liver disease, Non-B Non-C


title: 5097, chronic liver disease, Non-B Non-C


title: Sample 2_IL1-R1 KO 1d Control


title: 5025, chronic liver disease, Non-B Non-C


title: 5317, chronic liver disease, Non-B Non-C


title: 3983, chronic liver disease, Non-B Non-C


title: 4177, chronic liver disease, Non-B Non-C


title: 4636, chronic liver disease, Non-B Non-C


title: 4646, chronic liver disease, Non-B Non-C


title: 5171, chronic liver disease, Non-B Non-C


title: 4896, chronic liver disease, Non-B Non-C


title: 3845, chronic liver disease, Non-B Non-C


title: 3833, chronic liver disease, Non-B Non-C


title: 5181, chronic liver disease, Non-B Non-C


title: 5312, chronic liver disease, Non-B Non-C


title: 4469, chronic liver disease, Non-B Non-C


title: 3902, chronic liver disease, Non-B Non-C


title: 3460, chronic liver disease, Non-B Non-C


title: 3345, chronic liver disease, Non-B Non-C


title: 5142, chronic liver disease, Non-B Non-C


title: 4845, chronic liver disease, Non-B Non-C


title: 3114, chronic liver disease, Non-B Non-C


title: 3748, chronic liver disease, Non-B Non-C


title: 5229, chronic liver disease, Non-B Non-C


title: 3008, chronic liver disease, Non-B Non-C


title: 3814, chronic liver disease, Non-B Non-C


title: 4126, chronic liver disease, Non-B Non-C


title: 4321, chronic liver disease, Non-B Non-C


title: 2855, chronic liver disease, Non-B Non-C


title: 4687, chronic liver disease, Non-B Non-C


title: 4737, chronic liver disease, Non-B Non-C


title: 4889, chronic liver disease, Non-B Non-C


title: 3750, chronic liver disease, Non-B Non-C


title: 5116, chronic liver disease, Non-B Non-C


title: 4398, chronic liver disease, Non-B Non-C


title: 5258, chronic liver disease, Non-B Non-C


title: 5007, chronic liver disease, Non-B Non-C


title: 2643, chronic liver disease, Non-B Non-C


title: 5108, chronic liver disease, Non-B Non-C


title: 4971, chronic liver disease, Non-B Non-C


title: 4716, chronic liver disease, Non-B Non-C


title: 4877, chronic liver disease, Non-B Non-C


title: 4404, chronic liver disease, Non-B Non-C


title: 4610, chronic liver disease, Non-B Non-C


title: 4343, chronic liver disease, Non-B Non-C


title: 4097, chronic liver disease, Non-B Non-C


title: 3702, chronic liver disease, Non-B Non-C


title: 3661, chronic liver disease, Non-B Non-C


title: 3746, chronic liver disease, Non-B Non-C


title: 3780, chronic liver disease, Non-B Non-C


title: 3339, chronic liver disease, Non-B Non-C


title: 5231, liver, control

value: control


title: 3570, chronic liver disease, Non-B Non-C


title: 4699, liver, control


title: 4658, liver, control


title: 5233, liver, control


title: 5136, liver, control


title: 5150, liver, control


title: 5294, chronic liver disease, Non-B Non-C


title: 4293, liver, control


title: 4956, chronic liver disease, Non-B Non-C


title: 4983, liver, control


title: 5126, liver, control


title: 4455, liver, control


title: 4512, liver, control


title: R_PDO, single culture

city: Seongnam

first: Ji-Won

state: Gyeonggi-do

address: 82 Gumi-ro-173-beon-gil

department: Internal Medicine

institute: Seoul National University Bundang Hospital

description: Library name: R_PDO-HUVEC

data_processing:
Bulk RNA sequencing (RNA-seq) of the PDO and human umbilical vein endothelial cell (HUVEC) co-culture system was performed on the NovaSeq 6000 system (Illumina). Raw sequencing data were converted from .bcl to .fastq format, and low-quality reads were filtered using Fastp version 0.23.4. Filtered reads were aligned to the GRCh38 reference genome using STAR pipeline version 2.7.11b with "Basic" two-pass mode and Gencode V44 annotations. Duplicate reads were marked using Picard version 3.1.1, and gene expression was quantified using featureCounts version 2.0.6. Quality control was performed using Qualimap version 2.
Assembly: GRCh38
Supplementary files format and content: raw count files

extract_protocol:
We stained the cells with Celltracker blue and red (Invitrogen) according to the manufacturer's recommendation. Briefly, harvested cells were incubated with the serum-free media containing 1 µM Celltrackers for 30 min at 37°C. After washing with PBS, the stained cells were seeded for further experiments. Twenty-four-well plates coated with Matrigel Basement Membrane Matrix (Corning) were incubated at 37°C for 1 h. Then, 1 × 105 HUVECs suspended with CM were seeded on the 24-well plates. After 18 h, HUVECs were stained with Calcein-AM (Corning). The fluorescent images were captured using a fluorescence microscope (Zeiss, Göttingen, Germany) and analyzed using ZEN Blue software (Zeiss).
Library was constructed and sequenced using NovaSeq 6000 system

value: epithelial cell


title: R_PDO, co-cultured with HUVEC

description: Library name: R_PDO+HUVEC


title: P_PDO, single culture

description: Library name: P_PDO-HUVEC


title: 4187, liver, control


title: HUVEC, single culture

description: Library name: HUVEC-PDO

source_name: HUVEC

value: HUVEC

value: endothelial cell


title: 3441, chronic liver disease, Non-B Non-C


title: TFEB-KD, Rep1

city: Innsbruck

first: Pablo

last: Monfort-Lanzas

address: Innrain 80-82

department: Medical Biochemistry

country: Austria

institute: Medical University Innsbruck

description:
Library name: TFEB-KD-d4r1
Column name in raw_counts.tsv: TFEB.KD.tBHP.d4r1

data_processing:
Quality control and adapter trimming were performed using TrimGalore.
Reads were aligned to the human genome (hg38, GENCODE reference) using STAR (v2.7.10a).
Gene-level quantification was performed using Salmon (v1.10.1).
Differential gene expression analysis was conducted using DESeq2 (R package, v1.38.3).
Pathway enrichment and over-representation analysis were performed using ReactomePA (R package, v1.42.0).
Assembly: hg38 (GENCODE reference).
Supplementary files format and content: raw_counts.tsv (tab-delimited file containing raw read counts for each sample).
Supplementary files format and content: TPM_counts.tsv (TPM-normalized gene expression values).
Supplementary files format and content: DEG_results.csv (Differentially expressed genes (DEG) with log2 fold change, p-value, and adjusted p-value)

growth_protocol: HFF-2 human dermal fibroblasts were cultured in DMEM low glucose (Sigma, D5921) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Gibco, 10270-106), 4 mM glutamine (Sigma, G7513), and 1% penicillin/streptomycin (Sigma, P4333) in a humidified incubator at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted using the Monarch Total RNA Miniprep kit (NEB, T2010S) following the manufacturer's instructions. RNA integrity was verified using an Agilent Bioanalyzer.
RNA libraries were prepared using the SMARTer mRNA-Seq Library Prep Kit according to the manufacturer's protocol.

treatment_protocol:
HDFs were treated with 40 µM tert-butyl hydroperoxide (tBHP) for 1 hour, twice daily, over a span of four consecutive days.
TFEB knockdown was achieved using lentiviral transduction with PLKO shTFEB (NM_007162.1-1037s1c1) (Sigma) combined with psPAX2 (Addgene, #12260) and pMD2G/VSVG (Addgene, #12259) packaging plasmids. HDFs were selected with puromycin for stable knockdown.

value: Fibroblast

value: TFEB-KD

value: tBHP 40µM

tag: batch

value: Day 4


title: Scr Control, Rep3

description:
Library name: SCR-tBHP-d4r3
Column name in raw_counts.tsv: SCR.tBHP.d4r3

value: WT


title: TFEB-KD, Rep2

description:
Library name: TFEB-KD-d4r2
Column name in raw_counts.tsv: TFEB.KD.tBHP.d4r2


title: 4742, liver, control


title: HUVEC, co-cultured with R_PDO

description: Library name: HUVEC+R_PDO


title: P_PDO, co-cultured with HUVEC

description: Library name: P_PDO+HUVEC


title: testis, recolinized germ free, rep 2

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

description: Library name: RECOL_TESTIS_2

data_processing:
Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Reads were mapped using RSEM against the mus musculus genome (mm10) and normalized to transcripts per million (tpm).
Assembly: mm10
Supplementary files format and content: Excel spreadsheet (.xlsx) with each column normalized gene expression values (transcripts per million) for each sample.

source_name: testis

extract_protocol:
Total RNA was extracted from tissue samples using standard Trizol method.
Tissue was homogenized in Trizol and total RNA was extracted.
Illumina stranded mRNA prep kit

treatment_protocol: Adult (8-14 wk old) male mice reared in germ-free (GF) or typical conventional conditions (specific-pathogen free controls; SPF) and offspring of GF x SPF parents were sacrificed and dissected for the male reproductive tract. The testes, caput and cauda epididymis was further dissected, cleaned of fat and snap frozen ready for subsequent RNA extraction.

value: testis

value: germ-free, recolinized

tag: library construction

value: Illumina Stranded mRNA prep kit

tag: genome build


title: testis, recolinized germ free, rep 1

description: Library name: RECOL_TESTIS_1

tag: genotype


title: cauda epididymis, recolinized germ free, rep 3

description: Library name: RECOL_CAU_3

source_name: epididymis

value: epididymis

tag: segment

value: cauda (distal)


title: testis, recolinized germ free, rep 3

description: Library name: RECOL_TESTIS_3

tag: tissue


title: DT, replicate 4, scRNA seq

first: Menghui

address: No. 826, Zhangheng Road, Pudong New District, Shanghai, China.

institute: Fudan university

library_source: transcriptomic single cell

data_processing:
The raw reads obtained from scRNA-seq were processed through CeleScope (https://github.com/singleron-RD/CeleScope) v1.5.2 pipeline to generate gene expression matrixes. Besides,to obtain the barcode sequence of a single cell, we filtered the raw reads from the barcode library by retaining only those that contained the target sequence “AATCCAGCTAGCTGTGCAGC”, which served as a prefix for the intended barcode. Further analysis was conducted on the lineage barcodes that were annotated with Unique Molecular Identifiers (UMIs) using the R programming language.
Assembly: genome GRCh38
Supplementary files format and content: matrix files

source_name: Mouse xenograft tumor

extract_protocol:
The drug-naive tumors and sorafenib-treated tumors from NOD/SCID mice were minced on a plate and enzymatically digested with collagenase IV (#C5138, Sigma) and DNase I (#MB3069, Meilunbio) for 30 min at 37 ℃ with agitation. After digestion, samples were sieved through a 70 μm cell strainer. After staining with Propidium Iodide (PI), samples were sorted by BD FACSAria cell sorter (BD Biosciences, San Jose, CA) to obtain CopGFP-positive and PI-negative cells. The samples were stained with Trypan Blue and the cell viability was evaluated microscopically. Single-cell suspensions with phosphate-buffered saline (PBS) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System.
The scRNA-seq libraries and barcode libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron).

value: Mouse xenograft tumor

tag: cell type

value: Hepatocellular carcinoma cell

value: DT


title: cauda epididymis, recolinized germ free, rep 1

description: Library name: RECOL_CAU_1


title: cauda epididymis, recolinized germ free, rep 2

description: Library name: RECOL_CAU_2


title: DT, replicate 3, scRNA seq


title: DT, replicate 2, scRNA seq


title: DN, replicate 2, scRNA seq

value: DN


title: TFEB-KD, Rep3

description:
Library name: TFEB-KD-d4r3
Column name in raw_counts.tsv: TFEB.KD.tBHP.d4r3


title: DT, replicate 1, scRNA seq


title: HUVEC, co-cultured with P_PDO

description: Library name: HUVEC+P_PDO


title: caput epididymis, recolinized germ free, rep 3

description: Library name: RECOL_CAP_3

value: caput (proximal)


title: Scr Control, Rep2

description:
Library name: SCR-tBHP-d4r2
Column name in raw_counts.tsv: SCR.tBHP.d4r2


title: DN, replicate 1, scRNA seq


title: caput epididymis, recolinized germ free, rep 2

description: Library name: RECOL_CAP_2


title: Scr Control, Rep1

description:
Library name: SCR-tBHP-d4r1
Column name in raw_counts.tsv: SCR.tBHP.d4r1


title: caput epididymis, recolinized germ free, rep 1

description: Library name: RECOL_CAP_1


title: Liver-Immune-ATAC

city: Washington

first: Anton

last: Wellstein

state: DC

address: 3970 Reservoir Road, N.W.,

department: Oncology

institute: Georgetown University

description: ATAC-seq

data_processing:
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20”.
Trimmed paired-end FASTQ reads were mapped to the human genome (GRCh37/hg19 build) using Bowtie2-align (V 2.3.5.1) with parameters “-X 1000 --local --very-sensitive --no-mixed --dovetail --phred33”.
Duplicated reads were marked with Picard (V 2.18.14) and reads with low mapping quality, duplicated or not mapped in proper pair were excluded using Samtools view (V 1.12) with parameters “-F 1796 -q 30”. BAM files were sorted and indexed using Samtools.
Chromatin accessibility data was normalized to the same depth and then bigWig files were created using deepTools (V 3.5.1) (87) with the functions ‘multiBamSummary ‘ and ‘bamCoverage’ using parameters “--normalizeUsing RPKM --binSize 25”.
Detection q-values were calculated for histone modification data relative to Input control using the macs3 (V3.0.0a6) (88) bdgcmp function (-m qpois).
Assembly: hg19
Supplementary files format and content: bigWig files containing read-depth normalized signal and signal q-value information.

source_name: Liver

extract_protocol:
ATAC-seq: Cryopreserved cells were pelleted and incubated in Lysis Buffer. Intact nuclei then underwent Tagmentation Reaction and purifiaction.  Cut&Tag: Cryopreserved cells were bound to concanavalin A beads and incubated with H3K27ac antibody. Following antibody incubation, chromatin was sheared using pA-Tn5 transposome enzyme and then extracted DNA was used as input for library preparation.
ATAC-seq libraries were generated from liver sinusoidal endothelial (LSEC) and liver-resident immune cryopreserved cells using the ATAC-seq kit (Active Motif). H3K27ac histone modification data was generated from liver sinusoidal endothelial (LSEC) and liver-resident immune cryopreserved cells using the Cut&Tag-IT Assay kit (Active Motif, H3K27ac antibody cat#39133). Library products were assessed by Agilent Bioanalyzer HS DNA assays (Agilent Technologies, Inc.) and clustered on an Illumina Novaseq 6000 S4 flow cell followed by 150bp paired-end sequencing with inclusion of 10-15% spike-in PhiX Control v3 library (Illumina).

value: Liver

value: immune

value: healthy


title: LSEC-ATAC

description: ATAC-seq

value: endothelial


title: testis, specific pathogen free, set 2, rep 4

description: Library name: RECOL_CON_TESTIS_4

value: control


title: testis, specific pathogen free, set 2, rep 3

description: Library name: RECOL_CON_TESTIS_3


title: Liver-Immune-HHK-A

data_processing:
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20 --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10 --retain_unpaired -r1 20 -r2 20” (https://github.com/FelixKrueger/TrimGalore).
Trimmed paired-end FASTQ reads were mapped to the human genome  (GRCh37/hg19 build) using Bismark (V 0.22.3) with parameters “--non-directional” (Kreuger et al. 2011), then converted to BAM files using SAMtools (V 1.12) (Li et al., 2009). BAM files were sorted and indexed using Samtools (V1.12).
Reads were stripped from non-CpG nucleotides and converted to BETA and PAT files using wgbstools (V 0.1.0) (Loyfer and Kaplan, 2023).
Assembly: hg19
Supplementary files format and content: BETA, PAT, and index files were generated using wgbstools bam2pat (https://github.com/nloyfer/wgbs_tools) with default parameters
Supplementary files format and content: blocks file (bed) was generated using wgbstools segment, and then compressed and indexed using tabix (samtools)
Supplementary files format and content: UXMatlas file (TSV) was generated using uxm build (https://github.com/nloyfer/UXM_deconv) with parameters “--rlen 3”.

extract_protocol:
Genomic DNA from tissues was extracted with DNeasy Blood and Tissue Kit (Qiagen; Germantown, MD) following the manufacturer’s instructions and quantified via Qubit fluorometer dsDNA BR Assay Kit (ThermoFisher Scientific, Cat. No. Q32853). Extracted DNA was stored at  -20°C for bisulfite conversion and MCC-seq library preparation.
Genomic DNA was fragmented via sonification using a Covaris M220 instrument to the recommended target 150-200 base pairs and subject to bisulfite conversion using the Zymo EZ DNA Methylation Gold kit  (#D5005 Zymo Research, Irvine, CA). Whole Genome Bisulfite Sequencing libraries were generated using the Zymo Research Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research, Irvine, CA). WGBS libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA) and then pooled to meet the required 1ug DNA input necessary for targeted enrichment. Hybridization capture was carried out according to the SeqCap Epi Enrichment System protocol (Roche NimbleGen, Inc.; Pleasanton, CA) using xGen Universal Blocker-TS Mix (Integrated DNA Technologies, USA) as the blocking reagent and SeqCap Epi CpGiant probe pools (human) or SeqCap Epi Developer probe pools (mouse samples). MethylC-Capture Sequencing (MCC-seq) libraries were assessed using Qubit Fluorometer (ThermoFisher) and Agilent Bioanalyzer DNA 1000 assays (Agilent Technologies, Inc., USA). MCC-seq libraries with inclusion of 15-20% spike-in PhiX Control v3 library (Illumina; San Diego, CA) were clustered on a Illumina Novaseq 6000 S4 flow cell followed by 150-bp paired-end sequencing.
MCC-seq (MethylC-capture sequencing)

value: kupffer


title: LSEC-H3K27ac

description: H3K27ac signal q-value; H3K27ac read-depth normalized signal

data_processing:
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20”.
Trimmed paired-end FASTQ reads were mapped to the human genome (GRCh37/hg19 build) using Bowtie2-align (V 2.3.5.1) with parameters “-X 1000 --local --very-sensitive --no-mixed --dovetail --phred33”.
Duplicated reads were marked with Picard (V 2.18.14) and reads with low mapping quality, duplicated or not mapped in proper pair were excluded using Samtools view (V 1.12) with parameters “-F 1796 -q 30”. BAM files were sorted and indexed using Samtools.
Chromatin accessibility data was normalized to the same depth and then bigWig files were created using deepTools (V 3.5.1) (87) with the functions ‘multiBamSummary ‘ and ‘bamCoverage’ using parameters “--normalizeUsing RPKM --binSize 25”.
Detection q-values were calculated for histone modification data relative to Input control using the macs3 (V3.0.0a6) (88) bdgcmp function (-m qpois).
Assembly: hg19
Supplementary files format and content: bigWig files containing read-depth normalized signal and signal q-value information.
Library strategy: Cut&Tag


title: Keratinocyte-HKER-B

value: keratinocyte


title: testis, specific pathogen free, set 2, rep 2

description: Library name: RECOL_CON_TESTIS_2

value: testis

value: WT


title: testis, specific pathogen free, set 2, rep 1

description: Library name: RECOL_CON_TESTIS_1

value: Illumina Stranded mRNA prep kit


title: cauda epididymis, specific pathogen free, set 2, rep 4

description: Library name: RECOL_CON_CAU_4

value: epididymis


title: caput epididymis, specific pathogen free, set 2, rep 4

description: Library name: RECOL_CON_CAP_4


title: caput epididymis, specific pathogen free, set 2, rep 3

description: Library name: RECOL_CON_CAP_3


title: cauda epididymis, specific pathogen free, set 2, rep 3

description: Library name: RECOL_CON_CAU_3

value: cauda (distal)


title: cauda epididymis, specific pathogen free, set 2, rep 5

description: Library name: RECOL_CON_CAU_5


title: Keratinocyte-HKER-A


title: Hepatic-Stellate-HHSC-A

value: stromal


title: HiC, H9 cell line, without VEGF-A 48hr, rep2

value: human embryonic stem cells

value: endothelial differentiation


title: testis, specific pathogen free, set 2, rep 5

description: Library name: RECOL_CON_TESTIS_5


title: Liver-Immune-H3K27ac


title: cauda epididymis, specific pathogen free, set 2, rep 2

description: Library name: RECOL_CON_CAU_2


title: Dermal-Microvascular-Endothelial-HDMVEC-A

source_name: Skin

value: Skin


title: Liver-Immune-HHK-B


title: caput epididymis, specific pathogen free, set 2, rep 5

description: Library name: RECOL_CON_CAP_5

value: caput (proximal)


title: Biliary-Columnar-Epithelial-IntraHepatic-HIhBEC-B

source_name: Biliary

value: Biliary

value: biliary-epithelial


title: cauda epididymis, specific pathogen free, set 2, rep 1

description: Library name: RECOL_CON_CAU_1


title: Hepatic-Stellate-HHSC-B

value: Liver

value: healthy


title: HiC, H9 cell line, without VEGF-A 48hr, rep1


title: Dermal-Microvascular-Endothelial-HDMVEC-B

value: endothelial


title: Biliary-Columnar-Epithelial-IntraHepatic-HIhBEC-A


title: Biliary-Cuboidal-Epithelial-CommonBileDuct-HCBD-B


title: Biliary-Cuboidal-Epithelial-CommonBileDuct-HCBD-A


title: caput epididymis, specific pathogen free, set 2, rep 2

description: Library name: RECOL_CON_CAP_2

value: control


title: Biliary-Columnar-Epithelial-Gallbladder-HBEC-B


title: Biliary-Columnar-Epithelial-Gallbladder-HBEC-A


title: LTR144-FC-POD15

data_processing:
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20 --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10 --retain_unpaired -r1 20 -r2 20” (https://github.com/FelixKrueger/TrimGalore).
Trimmed paired-end FASTQ reads were mapped to the human genome  (GRCh37/hg19 build) using Bismark (V 0.22.3) with parameters “--non-directional” (Kreuger et al. 2011), then converted to BAM files using SAMtools (V 1.12) (Li et al., 2009). BAM files were sorted and indexed using Samtools (V1.12).
Reads were stripped from non-CpG nucleotides and converted to BETA and PAT files using wgbstools (V 0.1.0) (Loyfer and Kaplan, 2023).
Assembly: hg19
Supplementary files format and content: BETA, PAT, and index files were generated using wgbstools bam2pat (https://github.com/nloyfer/wgbs_tools) with default parameters

source_name: Serum

extract_protocol:
Circulating cell-free DNA was extracted from 4-6 mL human serum, using the QIAamp Circulating Nucleic Acid kit (Qiagen, Cat. No. 55114) according to the manufacturer’s instructions. Cell-free DNA was quantified via Qubit fluorometer using the dsDNA Assay Qubit fluorometer Kits (ThermoFisher Scientific, Cat. No. Q32853 and Q10212 respectively). As a quality control, fragment size distribution of isolated cfDNA was verified based on analysis using a 2100 Bioanalyzer TapeStation using either a High Sensitivity DNA Assay or DNA 1000 Assay (Agilent Technologies, Santa Cruz, CA, USA) dependent on concentration determined via either Qubit dsDNA BR or HS Assay. Additional purification using Beckman Coulter beads was implemented to remove high-molecular weight DNA reflective of cell-lysis and leukocyte contamination (Agencourt AMPure cat#A63880) (Maggi et al. 2018).
Cell-free DNA from serum was subject to bisulfite conversion using the Zymo EZ DNA Methylation Gold kit  (#D5005 Zymo Research, Irvine, CA). Whole Genome Bisulfite Sequencing libraries were generated using the Zymo Research Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research, Irvine, CA). WGBS libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA) and then pooled to meet the required 1ug DNA input necessary for targeted enrichment. Hybridization capture was carried out according to the SeqCap Epi Enrichment System protocol (Roche NimbleGen, Inc.; Pleasanton, CA) using xGen Universal Blocker-TS Mix (Integrated DNA Technologies, USA) as the blocking reagent and SeqCap Epi CpGiant probe pools (human) or SeqCap Epi Developer probe pools (mouse samples). MethylC-Capture Sequencing (MCC-seq) libraries were assessed using Qubit Fluorometer (ThermoFisher) and Agilent Bioanalyzer DNA 1000 assays (Agilent Technologies, Inc., USA). MCC-seq libraries with inclusion of 15-20% spike-in PhiX Control v3 library (Illumina; San Diego, CA) were clustered on a Illumina Novaseq 6000 S4 flow cell followed by 150-bp paired-end sequencing.
MCC-seq (MethylC-capture sequencing)

treatment_protocol: Liver transplant patients were enrolled and provided signed informed consent in this IRB approved study at Medstar Georgetown University Hospital (IRB protocols #2017-0690 and #2017-0365). Serial serum samples were collected from 28 liver transplant patients at predetermined timepoints; pre-transplant (PRE) and post-reperfusion (POST) on post-operative day 0 (POD0), post-operative day 7 (POD0), and post-operative day 30 (POD30). Beyond this, we also collected samples in patients experiencing complications at the time of symptom presentation. Further, we added phenotype-matched samples from an additional 16 patients at the time of for-cause liver biopsy (FC-bx) used to diagnose allograft injury. For serum isolation, peripheral blood (~6-12 mL) was collected in red-top venous puncture tubes and allowed to clot at room temperature for 30 minutes before centrifugation at 1500 x g for 20 min at 4ºC to separate the serum fraction. The serum was aliquoted in 0.5 mL fractions to avoid multiple freeze-thaw cycles and stored at −80ºC until use.

value: Serum


title: HiC, H9 cell line, without VEGF-A 12hr, rep2


title: caput epididymis, specific pathogen free, set 2, rep 1

description: Library name: RECOL_CON_CAP_1


title: cauda epididymis, germ free x control F1 offspring, rep 3

data_processing:
Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Assembly: mm10
Supplementary files format and content: Excel spreadsheet (.xlsx) with each column normalized gene expression values (transcripts per million) for each sample.

extract_protocol:
Total RNA was extracted from tissue samples using standard Trizol method.
Illumina stranded mRNA prep kit

value: F1 offspring of GF x SPF parents


title: LTR143-FC-POD29


title: LTR142-FC-POD91


title: HiC, H9 cell line, without VEGF-A 12hr, rep1

value: WT


title: cauda epididymis, germ free x control F1 offspring, rep 1


title: LTR140-FC-POD4


title: cauda epididymis, germ free x control F1 offspring, rep 2


title: LTR141-FC-POD5


title: LTR139-FC-POD44


title: LTR139-FC-POD2


title: HiC, H9 cell line, with VEGF-A 48hr, rep1


title: cauda epididymis, Rag2 KO, rep 3


title: HiC, H9 cell line, with VEGF-A 12hr, rep2


title: HiC, H9 cell line, with VEGF-A 48hr, rep2


title: LTR139-FC-POD21


title: cauda epididymis, Rag2 KO, rep 2


title: HiC, H9 cell line, with VEGF-A 12hr, rep1


title: LTR139-FC-POD29


title: LTR137-FC-POD18


title: LTR137-FC-POD42


title: cauda epididymis, Rag2 KO, rep 1


title: HiC, H9 cell line, Mesoderm, rep2


title: LTR136-FC-POD7


title: LTR138-FC-POD7


title: LTR135-FC-POD7


title: cauda epididymis, germ free, rep 6

value: germ-free


title: HiC, H9 cell line, hESC, rep2


title: LTR133-FC-POD13


title: LTR133-FC-POD125


title: cauda epididymis, germ free, rep 4

value: epididymis


title: HiC, H9 cell line, hESC, rep1


title: LTR130-FC-POD17


title: LTR128-POD7


title: cauda epididymis, germ free, rep 3

value: cauda (distal)


title: LTR132-FC-POD39


title: LTR129-FC-POD12


title: LTR128_plasma-POD7

source_name: Plasma

value: Plasma


title: LTR128-POD0-POST


title: cauda epididymis, germ free, rep 2


title: LTR128-POD0-PRE


title: cauda epididymis, specific pathogen free, rep 4


title: cauda epididymis, germ free, rep 1


title: LTR128_plasma-POD0-POST


title: LTR128-POD30


title: Alcohol-fed liver with AKAP12 vector , sample G1

city: Los Angeles

first: Komal

last: Ramani

state: CA

address: 8700 Beverly Blvd.

institute: Cedars-Sinai Medical Center

description:
Library name: G1
column name in raw counts_G1.counts.txt

data_processing:
Data were processed by Azenta Inc.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted by the services of Azenta Inc.
Libraries were constructed by Azenta Inc. and sequenced on Illumina platform

treatment_protocol: Mice were fed a control lieber-de carli or an ethanol diet for 10 days during which they were injected with an empty vector backbone or a CMV-AKAP12 vector using in vivo JETPEI gal reagent (polyplus-sartorius) at day 3, 6,9. On the 11th day of feeding, mice were oral gavaged with binge 5% alcohol and sacrificed after 9h. Livers were isolated and snap frozen

value: liver

value: Ethanol diet


title: WT liver with AKAP12 vector , sample C1

description:
Library name: C1
column name in raw counts_C1.counts.txt

value: Control diet


title: HiC, H9 cell line, Mesoderm, rep1

value: human embryonic stem cells

value: endothelial differentiation


title: cauda epididymis, germ free, rep 5


title: Alcohol-fed liver with Empty vector (EV) , sample E1

description:
Library name: E1
column name in raw counts_E1.counts.txt


title: LTR134-FC-POD70


title: Alcohol-fed liver with AKAP12 vector , sample H1

description:
Library name: H1
column name in raw counts_H1.counts.txt


title: LTR131-FC-POD8


title: WT liver with AKAP12 vector , sample D1

description:
Library name: D1
column name in raw counts_D1.counts.txt


title: LTR128_plasma-FC-POD1


title: LTR128-FC-POD1


title: LTR127-POD7


title: WT liver with Empty vector (EV) , sample B1

description:
Library name: B1
column name in raw counts_B1.counts.txt


title: LTR127-POD30


title: cauda epididymis, specific pathogen free, rep 3


title: cauda epididymis, specific pathogen free, rep 2


title: WT liver with Empty vector (EV) , sample A1

description:
Library name: A1
column name in raw counts_A1.counts.txt


title: LTR127-POD0-PRE


title: LTR127-FC-POD2


title: LTR127-POD0-POST


title: LTR126-POD0-PRE


title: LTR126-POD30


title: Meninges, Unstressed Control3

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
The fastq files of each RNA-seq data sample were aligned to theMus musculusGRCm38 transcriptomeusing STAR (version 2.7.5c)
The raw sequencing reads were quality assessed using fastp (version0.23.2), fastQC(version 0.11.9), and reported using multiqc (version 1.11)
Processed RNA-seq data was filtered, removing genes with low read counts(average counts >0.5)
Feature counts weretabulated with featureCounts (version 2.0.1).
Differential expression analysiswas done using EdgeR(version 3.42.4).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Meninges

extract_protocol:
RNA was isolated using the Picopure RNA Isolation Kit (Life Technologies) and quantified by the Qubit RNA HS Assay Kit (Thermo Fisher Scientific). 5 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Library Prep Kit according to the manufacturer's protocol.

treatment_protocol: Monocytes were isolated with the Milentyi MACS Monocyte Isolation Kit from the deep cervical lymph nodes and meninges of mice exposed to 18 days of chronic restraint stress. In cases with psychedelics, mice were exposed to 18 days of chronic restraint stress, administered vehicle, psilocybin, or MDMA, and allowed to sit for 24 hours before tissues were taken for processing.

value: Meninges

tag: Sex

value: Male

value: Monocyte


title: cauda epididymis, specific pathogen free, rep 1

tag: treatment


title: caput epididymis, germ free x control F1 offspring, rep 2

value: caput (proximal)


title: LTR126-POD7


title: LTR126_plasma-POD7


title: Meninges, Unstressed Control1


title: caput epididymis, germ free x control F1 offspring, rep 3


title: Meninges, Unstressed Control2


title: LTR126_plasma-FC-POD43


title: Stress, NoFear, Amygdala, Astrocyte, M5

data_processing:
The fastq files of each RNA-seq data sample were aligned to the Mus musculus GRCm38 transcriptome using STAR (version 2.7.5c)
The raw sequencing reads were quality assessed using fastp (version0.23.2), fastQC(version 0.11.9), and reported using multiqc (version 1.11)
Processed RNA-seq data was filtered, removing genes with low read counts (average counts <0.5)
Feature counts were tabulated with featureCounts (version 2.0.1).
Differential expression analysis was done using EdgeR (version 3.42.4).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Brain

treatment_protocol: The amygdala was dissected from mice with or without chronic restraint and with or without fear exposure and was digested in 500-uL of Hibernate-A containing 7.5-uL of papain. Tissue was dissociated and processed using the Milentyi MACS Anti-Acsa-2 Microbeads Kit. Mice were allowed to sit for 24 hours following the final day of behavior or stress before tissues were taken for processing.

value: Brain

value: Astrocyte


title: caput epididymis, Rag 2 KO, rep 1


title: LTR126_plasma-POD0-POST


title: Stress, NoFear, Amygdala, Astrocyte, M4


title: caput epididymis, Rag 2 KO, rep 2


title: LTR126-POD0-POST

value: Serum


title: caput epididymis, germ free x control F1 offspring, rep 1

value: WT

value: F1 offspring of GF x SPF parents


title: LTR126-FC-POD43


title: LTR125-POD7


title: Stress, NoFear, Amygdala, Astrocyte, M3


title: LTR125-POD30


title: caput epididymis, germ free, rep 6

value: epididymis

value: germ-free


title: LTR125-POD0-PRE


title: Stress, NoFear, Amygdala, Astrocyte, M2


title: LTR125-POD0-POST


title: caput epididymis, germ free, rep 5


title: LTR125_plasma-POD7

value: Plasma


title: LTR125_plasma-POD0-POST


title: caput epididymis, germ free, rep 4


title: LTR125_plasma-FC-POD15


title: Stress, NoFear, Amygdala, Astrocyte, M1


title: caput epididymis, germ free, rep 3


title: LTR124-POD0-POST


title: LTR124-POD0-PRE


title: Stress, Fear, Amygdala, Astrocyte, M5


title: LTR125-FC-POD15


title: LTR125-FC-POD9


title: LTR124-POD30


title: Stress, Fear, Amygdala, Astrocyte, M3


title: Stress, Fear, Amygdala, Astrocyte, M4


title: caput epididymis, germ free, rep 2


title: LTR124-FC-POD7


title: caput epididymis, germ free, rep 1


title: LTR123-POD30


title: Stress, Fear, Amygdala, Astrocyte, M2


title: caput epididymis, specific pathogen free, rep 4

value: control


title: LTR123-POD7


title: Stress, Fear, Amygdala, Astrocyte, M1


title: LTR123-POD15


title: caput epididymis, specific pathogen free, rep 3


title: LTR123-POD0-PRE


title: caput epididymis, specific pathogen free, rep 2


title: LTR123-POD0-POST


title: NoStress, Fear, Amygdala, Astrocyte, M4


title: LTR122-POD7


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day12, replicate 4, RNAseq

city: Galveston

first: Lynn

last: Soong

state: TX

address: 301 University Blvd MRB 3.132

institute: University of Texas Medical Branch

description:
Library name: D12_G4
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution

data_processing:
Provided by Novogene:  2. Bioinformatics Analysis Pipeline 2.1 Data quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. 2.2 Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built 2 using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. 2.3 Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. 2.4 Differential expression analysis For DESeq2 with biological replicates: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package (1.20.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The corrected P-value ≤ 0.05 & |log2 (foldchange)| ≥ 1 was set as the threshold of significant differential expression. 3 For edgeR without biological replicates: Prior to differential gene expression analysis, for each sequencing library, read counts were adjusted using the edgeR R package (3.22.5) by scaling normalization factors to eliminate differences in sequencing depth between samples, followed by differential expression analysis. The resulting P value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The corrected P-value ≤ 0.05 & |log2 (foldchange)| ≥ 1wasset as the threshold of significant differential expression. 2.5 GO and KEGG enrichment analysis of differentially expressed genes Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways 4 with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway. 2.6 Gene Set Enrichment Analysis Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre-defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO、KEGG、 Reactome、DO and DisGeNET data sets were used for GSEA independently.
Assembly: mm10
Supplementary files format and content: tab-delimited text file matrix includes FPKM values (the adjusted readcounts of all samples)

source_name: Spleen

extract_protocol:
Female C57BL/6J mice (8-12 weeks-old, purchased from the Jackson Laboratory #000664) were intravenously inoculated with 6.8 × 104 FFU, 200 µl of Karp or Gilliam strain, or PBS (mock). Mice were sacrificed at established timepoints, and spleens were collected in RPMI 1640 medium. Spleens were then stored in RNALater. Total RNA was extracted by using the RNeasy Mini kit (Qiagen). Total RNA (≥ 1ug) was sent to Novogene (Sacramento, CA) for Poly(A) RNA-Seq Sequencing Service.
Provided by Novogene: Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Spleen

value: Spleen cells

value: O. tsutsugamushi Gilliam strain


title: LTR122-POD0-PRE


title: LTR122-FC-POD30


title: NoStress, Fear, Amygdala, Astrocyte, M2


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day12, replicate 1, RNAseq

description:
Library name: D12_G1
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day12, replicate 3, RNAseq

description:
Library name: D12_G3
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: NoStress, Fear, Amygdala, Astrocyte, M3


title: LTR121-POD7


title: NoStress, NoFear, Amygdala, Astrocyte, M5


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day12, replicate 2, RNAseq

description:
Library name: D12_G2
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: testis, germ free, rep 3

value: testis


title: testis, specific pathogen free, rep 3


title: NoStress, NoFear, Amygdala, Astrocyte, M4


title: testis, germ free, rep 2


title: LTR122-POD0-POST


title: testis, germ free, rep 1


title: LTR121-POD30


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day12, replicate 4, RNAseq

description:
Library name: D12_K4
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution

value: O. tsutsugamushi Karp strain


title: LTR123-FC-POD124


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day12, replicate 3, RNAseq

description:
Library name: D12_K3
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: caput epididymis, specific pathogen free, rep 1


title: testis, germ free, rep 4


title: NoStress, Fear, Amygdala, Astrocyte, M1

value: Male


title: LTR121-POD0-PRE


title: NoStress, Fear, Amygdala, Astrocyte, M5


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day12, replicate 2, RNAseq

description:
Library name: D12_K2
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: testis, specific pathogen free, rep 2


title: NoStress, NoFear, Amygdala, Astrocyte, M2


title: NoStress, NoFear, Amygdala, Astrocyte, M3


title: LTR121-POD0-POST


title: testis, specific pathogen free, rep 1


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day8, replicate 4, RNAseq

description:
Library name: D8_G4
no raw data, files were corrupt


title: LTR120-POD7


title: NoStress, NoFear, Amygdala, Astrocyte, M1


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day8, replicate 3, RNAseq

description:
Library name: D8_G3
D8_G3_2.fastq.gz was corrupt


title: wtbud-1

city: Zhengzhou

first: Wei

last: Zhu

address: 100 Science Avenue

institute: Zhengzhou University

data_processing:
Trim Smart-seq2 public primer sequence from the Reads
The reference genomes and the annotation file were downloaded from Brassicaceae Database (http://brassicadb.cn). Bowtie v1.0.1 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2.
Reads Count for each gene in each sample was counted by featureCounts v2.0.1, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: Brassica rapa (http://brassicadb.cn)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica rapa

source_name: bud

growth_protocol: The wild type and transgenic B. rapa plants were grown in pots containing a soil: vermiculite mixture (3:1) in a controlled artificial climatic chamber (16 h light/8 h dark photoperiod at 21 °C/18 °C).

extract_protocol:
The stems and buds were collected,and RNA was harvested using Trizol reagent. 5–10 μg total RNA was used as the template for constructing RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: bud

tag: age

value: wild type


title: LTR120-POD0-PRE


title: Amygdala, sgEgfr_2, 7D Stress and Fear Conditioning (neuron RNA-seq)

data_processing:
The fastq files of each RNA-seq data sample were aligned to theMus musculusGRCm38 transcriptomeusing STAR (version 2.7.5c)
The raw sequencing reads were quality assessed using fastp (version0.23.2), fastQC(version 0.11.9), and reported using multiqc (version 1.11)
Processed RNA-seq data was filtered, removing genes with low read counts(average counts >0.5)
Feature counts were tabulated with featureCounts (version 2.0.1).
Differential expression analysiswas done using EdgeR(version 3.42.4).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Brain (amygdala)

treatment_protocol: AAV-targeting sgRosa or sgEgfr in astrocytes and sgRosa or sgAreg in microglia were transduced in the amygdala of C57BL/6J mice and allowed to express for >2 weeks. Mice were subsequently exposed to 7D of tube restraint followed by 1 day of fear conditioning and 3 days of fear extinction. The amygdala was digested in 500-uL of Hibernate-A containing 7.5-uL of papain. Tissue was dissociated and processed using the Milentyi MACS Adult Neuron Isolation Kit.

value: Brain (amygdala)

value: Neuron

tag: strain

value: sgEgfrAstro


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day8, replicate 2, RNAseq

description:
Library name: D8_G2
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: LTR120-POD30

value: Serum


title: wtbud-2


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day8, replicate 1, RNAseq

description:
Library name: D8_G1
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: Amygdala, sgEgfr_3, 7D Stress and Fear Conditioning (neuron RNA-seq)


title: sbud-3

value: BrCHR39-silenced lines


title: Amygdala, sgRosa_3, 7D Stress and Fear Conditioning (neuron RNA-seq)


title: LTR120-POD0-POST


title: LTR119-POD7


title: Amygdala, sgEgfr_1, 7D Stress and Fear Conditioning (neuron RNA-seq)


title: sbud-2


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day8, replicate 4, RNAseq

description:
Library name: D8_K4
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: Amygdala, sgRosa_2, 7D Stress and Fear Conditioning (neuron RNA-seq)


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day12, replicate 1, RNAseq

description:
Library name: D12_K1
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: wtbud-3


title: LTR119-POD30


title: sbud-1


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day8, replicate 3, RNAseq

description:
Library name: D8_K3
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day8, replicate 2, RNAseq

description:
Library name: D8_K2
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: LTR119-POD0-POST


title: Amygdala, sgNr2f2_3, 7D Stress and Fear Conditioning (RNA-seq)

extract_protocol:
RNA from neurons isolated with the Miltenyi MACS Adult Neuron Isolation Kit was isolated using the Picopure RNA Isolation Kit (Life Technologies) and quantified by the Qubit RNA HS Assay Kit (Thermo Fisher Scientific). 5 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Library Prep Kit according to the manufacturer's protocol.

treatment_protocol: AAV-targeting sgRosa or sgNr2f2 were transduced in the amygdala of C57BL/6J mice and allowed to express for >2 weeks. Mice were subsequently exposed to 7D of tube restraint followed by 1 day of fear conditioning and 3 days of fear extinction. The amygdala was digested in 500-uL of Hibernate-A containing 7.5-uL of papain. Tissue was dissociated and processed using the Milentyi MACS Adult Neuron Isolation Kit.

value: Brain


title: wtstem-2

source_name: stem

value: stem


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day8, replicate 1, RNAseq

description:
Library name: D8_K1
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: LTR118-POD30


title: sstem-3


title: LTR118-POD0-PRE


title: Amygdala, sgNr2f2_2, 7D Stress and Fear Conditioning (RNA-seq)


title: LTR118-POD7


title: LTR118-POD0-POST


title: Amygdala, sgNr2f2_1, 7D Stress and Fear Conditioning (RNA-seq)


title: wtstem-3


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day4, replicate 3, RNAseq

description:
Library name: D4_G3
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: Amygdala, sgRosa_4, 7D Stress and Fear Conditioning (RNA-seq)

value: sgRosa


title: Amygdala, sgRosa_1, 7D Stress and Fear Conditioning (neuron RNA-seq)


title: wtstem-1


title: Amygdala, sgRosa_3, 7D Stress and Fear Conditioning (RNA-seq)


title: sstem-2


title: LTR119-POD0-PRE


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day4, replicate 4, RNAseq

description:
Library name: D4_G4
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day4, replicate 1, RNAseq

description:
Library name: D4_G1
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: Spleen, O. tsutsugamushi Gilliam-infected C57BL/6 mice, Day4, replicate 2, RNAseq

description:
Library name: D4_G2
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day4, replicate 4, RNAseq

description:
Library name: D4_K4
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: LTR117-POD7


title: HumanMonocyte_LPS+MDMA3

data_processing:
The fastq files of each RNA-seq data sample were aligned to the hg19 human genome.
The raw sequencing reads were quality assessed using fastp (version0.23.2), fastQC(version 0.11.9), and reported using multiqc (version 1.11)
Processed RNA-seq data was filtered, removing genes with low read counts(average counts >0.5)
Feature counts weretabulated with featureCounts (version 2.0.1).
Differential expression analysiswas done using EdgeR(version 3.42.4).
Assembly: hg19
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: PBMCs

treatment_protocol: Human monocytes purified from PBMCs were obtained from iQ Biosciences. Cells were plated for 24 hours and then treated for 6-hours with PBS, LPS, Psilocybin, MDMA, Psilocybin+LPS, or MDMA+LPS.

value: PBMCs

value: Monocyte

value: LPS+MDMA


title: sstem-1


title: Amygdala, sgRosa_1, 7D Stress and Fear Conditioning (RNA-seq)


title: LTR117-POD30


title: Amygdala, sgRosa_2, 7D Stress and Fear Conditioning (RNA-seq)


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day4, replicate 3, RNAseq

description:
Library name: D4_K3
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution

value: Spleen

value: Spleen cells


title: Neuron, sgNr2f2, 7d Stress4

data_processing:
Duplicate reads were removed with Picard MarkDuplicates (version 2.25.2)
Raw sequencing read quality was assessed using fastp (version 0.23.2), fastQC (version 0.11.9), and reported using multiQC (version 1.11).
Peaks were called by Macs2 (version 2.2.9.1).
Peak differential analysis was done using DiffBind (version 3.10.0)
Motif enrichment and annotation was performed with Homer (version 4.10).
Assembly: mm10
Supplementary files format and content: macs narrowpeaks for each sample

extract_protocol:
Nuclei from neurons isolated with the Miltenyi MACS Adult Neuron Isolation Kit were transposed and DNA was amplified.
Libraries were sequenced using paired-end sequencing on an Illumina NextSeq550.


title: HumanMonocyte_LPS+MDMA1


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day4, replicate 1, RNAseq

description:
Library name: D4_K1
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution

value: O. tsutsugamushi Karp strain


title: LTR117-POD0-POST


title: Spleen, O. tsutsugamushi Karp-infected C57BL/6 mice, Day4, replicate 2, RNAseq

description:
Library name: D4_K2
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: Neuron, sgNr2f2, 7d Stress2

value: Male


title: HumanMonocyte_LPS+Psilocybin3

value: LPS+Psilocybin


title: HumanMonocyte_LPS+Psilocybin2


title: LTR116-POD7


title: Spleen, PBS mock-infected C57BL/6 mice, Day0, replicate 3, RNAseq

description:
Library name: Mock_3
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution

value: PBS


title: HumanMonocyte_LPS+Psilocybin1


title: Neuron, sgRosa, 7d Stress4


title: Spleen, PBS mock-infected C57BL/6 mice, Day0, replicate 4, RNAseq

description:
Library name: Mock_4
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: LTR116-POD0-PRE


title: LTR116-POD30


title: Spleen, PBS mock-infected C57BL/6 mice, Day0, replicate 2, RNAseq

description:
Library name: Mock_2
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: HumanMonocyte_MDMA3

value: MDMA


title: Neuron, sgRosa, 7d Stress2

value: Neuron


title: LTR116-POD0-POST


title: HumanMonocyte_LPS+MDMA2