title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026593LR01-GC2-1-8-31]

description: Valproate, 500 mg/kg, Day 6, Repeat 1

value: Valproate, 500 mg/kg, Day 6, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026592LR01-GC1-3-8-31]

status: Public on Dec 13 2023

type: SRA

city: Houston

first: yi

last: chai

address: pgpr

country: USA

institute: Biostate AI

description: Valproate, 250 mg/kg, Day 6, Repeat 3

library_source: transcriptomic

data_processing:
Raw data from Illumina sequencer
illumina Adaptor Trim
HISAT2 Alignment
Assembly: NCBI GCF_015227675.2, Genome assembly mRatBN7.2
Supplementary files format and content: csv

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Blood

growth_protocol: Animals were kept under a standard condition with room temperature at 21-23 ºC, 40-70% relative humidity, and a 12/12h light: dark cycle. Chow and water are available ad libitum.

extract_protocol:
Trizol based total RNA extraction method
RNA libraries for RNA-Seq were prepared by using mRNA capture based standard library preparation kit (Vazyme) following manufacturer's protocol.

tag: age

value: 8 wks

tag: Sex

value: male

tag: tissue

value: whole blood

tag: treatment

value: Valproate, 250 mg/kg, Day 6, Repeat 3


title: AL078604.2_MDAMB468_control_rep3

type: RNA

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 11F11, 5850 College Street

department: Pathology

country: Canada

institute: Dalhousie University

description: Gene expression from MDA-MB-468 cells with control ASO treatment

hyb_protocol: The purified RNA samples were then sent to The Centre for Applied Genomics (TCAG), located at The Hospital for Sick Children in Toronto, Canada. The RNA samples underwent reverse transcription into complementary DNA (cDNA) and were subsequently hybridized to the Affymetrix Human Gene 2.0 ST microarray platform.

scan_protocol: Affymetrix GeneChip Scanner 3000 (Scanner#4).

data_processing: Raw CEL files were processed using the Transcriptome Analysis Console (Affymetrix).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MDA-MB-468 cells

label_protocol: Sample were prepared with the Affymetrix WT PLUS Kit and labeled with Biotin Allonamide Triphosphate.

growth_protocol: Cells were cultured in a humidified incubator at 37C, with 5% CO2 in culture media, supplemented with 10% FBS.

extract_protocol: Cells were collected in TRIzol and RNA purified using a PureLink RNA kit (Invitrogen Thermo Fisher Scientific) following the manufacturer’s instructions.

treatment_protocol: Cells were treated for 48 hours with 15nM screening-grade modified antisense oligonucleotices GapmeRs, (Qiagen) admixed with TransIT-BrCa (MS Biolnyx) as per the manufacturer’s instructions.

tag: cell line

value: Control ASO


title: AL078604.2_MDAMB468_kd_rep1

description: Gene expression from MDA-MB-468 cells with AL078604.2 knockdown

value: anti-AL078604.2 ASO


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026599LR01-GA1-1-9-1]

description: Carbon tetrachloride, 0.5 ml/kg, Day 7, Repeat 1


title: AL078604.2_MDAMB468_control_rep1


title: 3543_OF1A_2-1-M1-H1

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

molecule: genomic DNA

source_name: OF1A human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-1-M1-K14


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026591LR01-GC1-2-8-31]

description: Valproate, 250 mg/kg, Day 6, Repeat 2

value: Valproate, 250 mg/kg, Day 6, Repeat 2


title: 3543_OF1A_2-1-M1-H13


title: 3543_OF1A_2-1-M1-H14


title: 3543_OF1A_2-1-M1-G2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026590LR01-GC1-1-8-31]

description: Valproate, 250 mg/kg, Day 6, Repeat 1

value: Valproate, 250 mg/kg, Day 6, Repeat 1


title: 3543_OF1A_2-1-M1-G1


title: 3543_OF1A_2-1-M1-G14


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026589LR01-GA4-3-8-31]

description: Carbon tetrachloride, 2 ml/kg, Day 6, Repeat 3


title: 3543_OF1A_2-1-M1-G13


title: AL078604.2_MDAMB231_kd_rep3

description: Gene expression from MDA-MB-231 cells with AL078604.2 knockdown

source_name: MDA-MB-231 cells


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026588LR01-GA4-2-8-31]

description: Carbon tetrachloride, 2 ml/kg, Day 6, Repeat 2


title: 3543_OF1A_2-1-M1-F2


title: AL078604.2_MDAMB468_kd_rep2


title: AL078604.2_MDAMB231_kd_rep2


title: AL078604.2_MDAMB231_kd_rep1


title: AL078604.2_MDAMB231_control_rep3

description: Gene expression from MDA-MB-231 cells with control ASO treatment


title: AL078604.2_MDAMB468_control_rep2


title: 3543_OF1A_2-1-M1-F14


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026587LR01-GA4-1-8-31]

description: Carbon tetrachloride, 2 ml/kg, Day 6, Repeat 1


title: 3543_OF1A_2-1-M1-F1


title: 3543_OF1A_2-1-M1-F13


title: 3543_OF1A_2-1-M1-E2


title: 3543_OF1A_2-1-M1-E1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026586LR01-GA3-3-8-31]

description: Carbon tetrachloride, 1.5 ml/kg, Day 6, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026585LR01-GA3-2-8-31]

description: Carbon tetrachloride, 1.5 ml/kg, Day 6, Repeat 2


title: 3543_OF1A_2-1-M1-E14


title: 3543_OF1A_2-1-M1-E13


title: 3543_OF1A_2-1-M1-D2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026584LR01-GA3-1-8-31]

description: Carbon tetrachloride, 1.5 ml/kg, Day 6, Repeat 1


title: AL078604.2_MDAMB231_control_rep1


title: 3543_OF1A_2-1-M1-D14


title: 3543_OF1A_2-1-M1-D1


title: 3543_OF1A_2-1-M1-D13


title: 3543_OF1A_2-1-M1-C2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026582LR01-GA2-2-8-31]

description: Carbon tetrachloride, 1 ml/kg, Day 6, Repeat 2


title: AL078604.2_MDAMB231_control_rep2


title: LINC01269_kd_rep2

description: Gene expression from SKBR3 cells with LINC01269 knockdown

source_name: SKBR3 cells

value: anti-LINC01269 ASO


title: 3543_OF1A_2-1-M1-C1


title: 3543_OF1A_2-1-M1-C13


title: 3543_OF1A_2-1-M1-B2


title: 3543_OF1A_2-1-M1-B1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026581LR01-GA2-1-8-31]

description: Carbon tetrachloride, 1 ml/kg, Day 6, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026580LR01-GA1-3-8-31]

description: Carbon tetrachloride, 0.5 ml/kg, Day 6, Repeat 3


title: 3543_OF1A_2-1-M1-B13


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026579LR01-GA1-2-8-31]

description: Carbon tetrachloride, 0.5 ml/kg, Day 6, Repeat 2


title: 3543_OF1A_2-1-M1-A1


title: 3543_OF1A_2-1-M1-A2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026578LR01-GA1-1-8-31]

description: Carbon tetrachloride, 0.5 ml/kg, Day 6, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026583LR01-GA2-3-8-31]

description: Carbon tetrachloride, 1 ml/kg, Day 6, Repeat 3


title: p14 & p16 knockdown, rep1

city: Würzburg

first: Jonas

last: Wohlfarth

state: Bavaria

address: Josef-Schneider-Str. 2

department: Dermatology

country: Germany

institute: University Hospital Würzburg

description:
p14_p16kd_19
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)

data_processing:
llumina reads were quality- and adapter-trimmed via Cutadapt version 2.5 using a cutoff Phred score of 20 in NextSeq mode and reads without any remaining bases were discarded.
Processed reads were mapped to the human genome GCF_000001405.40_GRCh38.p14 with splice junction-sensitive read mapper STAR version 2.7.2b  using default parameters.
Read counts on exon level summarized for each gene were generated using featureCounts v1.6.4 from the Subread package.
Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature.
Read abundance estimation and their differential expression were analyzed between axon and soma sample libraries using DESeq2 version 1.24.0. Read counts were normalized by DESeq2.
Assembly: human genome GCF_000001405.40_GRCh38.p14
Supplementary files format and content: raw_read_count.xlsx: xlsx file:  Raw read table

growth_protocol: MaMel51 with scr, p14kd, p16kd or p14/p16kd shRNA were kept in RPMI-1640 medium + 10 % FBS and 1 % penicillin/streptomycin in tissue culture flasks. Cells were then treated with 2 µg/ml doxycycline and placed in a 5% CO2, 37°C incubator for 4 day

extract_protocol:
RNA was isolated using the Direct-zol RNA Miniprep Kit (Zymo Research; Freiburg, Germany)
DNA libraries suitable for sequencing were prepared from 400 ng of total RNA, with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (½ volume)

treatment_protocol: MaMel51 with scr, p14kd, p16kd or p14/p16kd shRNA were plated in RPMI-1640 medium + 10 % FBS and 1 % penicillin/streptomycin in 6 well tissue culture flasks. Cells were then treated with 2 µg/ml doxycycline and placed in a 5% CO2, 37°C incubator for 4 days. After 4 days, medium was replaced with fresh medium + 2 µg/ml doxycyclin for 2 days

tag: cell type

value: Melanoma cell line

tag: genotype

value: p14 & p16 knockdown


title: p14 & p16 knockdown, rep2

description:
p14_p16kd_20
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)


title: p14 & p16 knockdown, rep3

description:
p14_p16kd_21
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)


title: LINC01269_control_rep2

description: Gene expression from SKBR3 cells with control ASO treatment


title: 3543_OF1A_2-1-M1-A14


title: LINC01269_kd_rep3


title: LINC01269_kd_rep1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026577LR01-1-3-8-31]

description: Sodium chloride, 0.9%, Day 6, Repeat 3

value: Sodium chloride, 0.9%, Day 6, Repeat 3


title: 3543_OF1A_2-1-M1-A13


title: p16 knockdown, rep3

description:
p16kd_9
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)

value: p16 knockdown


title: LINC01269_control_rep1


title: 3543_OF1A_1-6-I1-P24


title: LINC01269_control_rep3


title: p16 knockdown, rep2

description:
p16kd_8
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026576LR01-1-2-8-31]

description: Sodium chloride, 0.9%, Day 6, Repeat 2

value: Sodium chloride, 0.9%, Day 6, Repeat 2


title: 3543_OF1A_1-6-I1-P23


title: 3543_OF1A_1-6-I1-P12


title: 3543_OF1A_2-1-M1-B14


title: 3543_OF1A_1-6-I1-P11


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026575LR01-1-1-8-31]

description: Sodium chloride, 0.9%, Day 6, Repeat 1

value: 8 wks

value: Sodium chloride, 0.9%, Day 6, Repeat 1


title: p16 knockdown, rep1

description:
p16kd_7
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)


title: 3543_OF1A_1-6-I1-O24


title: p14 knockdown, rep3

description:
p14kd_15
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)

value: p14 knockdown


title: 3543_OF1A_1-6-I1-O12


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026574LR01-GC4-1-8-30]

description: Valproate, 1000 mg/kg, Day 5, Repeat 1

value: male

value: whole blood

value: Valproate, 1000 mg/kg, Day 5, Repeat 1


title: p14 knockdown, rep2

description:
p14kd_14
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)


title: 3543_OF1A_1-6-I1-O11

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-6-I1-N24

value: Female


title: p14 knockdown, rep1

description:
p14kd_13
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026573LR01-GC2-2-8-30]

description: Valproate, 500 mg/kg, Day 5, Repeat 2

value: Valproate, 500 mg/kg, Day 5, Repeat 2


title: ISC2_miRNA

city: Guangzhou

first: Ye-Guang

last: Chen

address: 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Quality control was performed using FastQC v0.19.7.
For bulk RNA-seq, sequencing reads were aligned to mm10 mouse genome reference (GRCh38) using STAR with default parameter (Dobin et al., 2013).
For small RNA-seq, clean data was mapped to mm10 mouse genome reference (GRCh38) and miRbase with Bowtie2 and the counts were summarized and normalized by RDeseq2.
Assembly: Sequencing reads were aligned using GRCm38/mm10 assembly of the mouse genome.
Supplementary files format and content: gene_count_matrix.csv: Comma-delimited text file includes reads counts for each sample.

organism: Mus musculus

source_name: Intestinal epithelial cells

growth_protocol: Villin-creERT; Lgr5-EGFP-IRES-creERT2; Dgcr8loxP/loxP intestinal organoids were stimulated with 4-OHT or ethanol for 24 hours and then cultured in ENR medium for an additional 3 days. Intestinal organoids and sorted Lgr5-GFPhigh ISCs were collected. Intestinal epithelial cells from WT and epithelial Dgcr8 knockout mice were also collected.

extract_protocol:
Total RNA was extracted and purified by using TRIZOL reagent (Thermo Fisher Scientific). 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA integrity was measured using electrophoresis. Subsequently, First-strand cDNA was generated using random hexamer primers. Then, a second-strand cDNA was synthesized. A-Tailing Mix and RNA Index Adapters followed to subjected to the end of the cDNA. The cDNA fragments were amplified by PCR and the product was qualified by Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and the 2100 Bioanalyzer (Agilent). After it, the products were denatured and circularized to collect the final library.
Bulk RNA-seq and small RNA-seq

treatment_protocol: WT and epithelial Dgcr8 knockout mice (8-10 weeks old) were applied with 5-FU (HY-90006, MCE) administration for consecutive 2 days, and intestinal crypts were collected one day after 5-FU administration.

value: Intestinal epithelial cells

value: WT

value: No


title: 3543_OF1A_1-6-I1-N23

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026572LR01-GC2-1-8-30]

description: Valproate, 500 mg/kg, Day 5, Repeat 1

value: Valproate, 500 mg/kg, Day 5, Repeat 1


title: Scr control, rep3

description:
Control_3
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)

value: Melanoma cell line

value: Scr control


title: Scr control, rep2

description:
Control_2
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)


title: 3543_OF1A_1-6-I1-N12


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026571LR01-GC1-3-8-30]

description: Valproate, 250 mg/kg, Day 5, Repeat 3

value: Valproate, 250 mg/kg, Day 5, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026570LR01-GC1-2-8-30]

description: Valproate, 250 mg/kg, Day 5, Repeat 2

value: 8 wks

value: Valproate, 250 mg/kg, Day 5, Repeat 2


title: Feces_DR_wild_mouse_community_with_Bifidobacteria_rep4

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

data_processing:
16S data were analyzed using QIIME 2 (v2020.2). Briefly, reads were denoised using the q2-dada2 plugin (exact parameters were forward reads truncated to 240 bases with 20 bases trimmed from the 5’ end, reverse reads truncated to 150 bases with 20 bases trimmed from the 5’ end, and bases truncated with quality score below 10). Using the q2-feature-table plugin, samples were rarefied to the depth of the sample with the fewest reads (>20,000 reads), and sequence variants were filtered if they did not occur in at least 4 samples. Rooted phylogenetic trees were generated using the align-to-tree-mafft-fasttree method in the q2-phylogeny plugin. Alpha and beta diversity analyses were performed using the core-metrics-phylogenetic method in the q2-diveristy plugin, with a sampling depth of 10,000 reads. Taxonomy was assigned to sequence variants using the q2-feature-classifier plugin and a naive Bayes classifier pre-trained on the SILVA 132 515F/806R 99% OTUs provided as a QIIME 2 data resource. A pseudocount of 1 was applied prior to calculating the fold change in the relative abundance of each taxonomic group. Significance was calculated using a custom R script to perform the Mann Whitney test for each taxonomic group.
Supplementary files format and content: tab delimited text - list of taxa abundance in all samples
Library strategy: 16s rRNA-seq

organism: feces metagenome

source_name: mouse feces

extract_protocol:
DNA was extracted from fecal pellets using phenol:chloroform or the MagAttract PowerMicrobiome DNA/RNA Kit.
16S V4 rDNA libraries were prepared using the Phusion High-Fidelity PCR Master Mix with primers 515F and 806R, and sequenced on an Illumina MiSeq instrument by the NIAID Microbiome Program core facility.

value: dietary restriction

tag: strain

tag: bacterial community

value: wild mouse community with Bifidobacteria

value: feces


title: ISC1_miRNA


title: 3543_OF1A_1-6-I1-M24


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026569LR01-GC1-1-8-30]

description: Valproate, 250 mg/kg, Day 5, Repeat 1

value: male

value: whole blood

value: Valproate, 250 mg/kg, Day 5, Repeat 1


title: 3543_OF1A_1-6-I1-O23

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Feces_DR_wild_mouse_community_with_Bifidobacteria_rep2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026568LR01-GA4-3-8-30]

description: Carbon tetrachloride, 2 ml/kg, Day 5, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026567LR01-GA4-2-8-30]

description: Carbon tetrachloride, 2 ml/kg, Day 5, Repeat 2


title: Normali skin fibroblasts - Sample20 [S20]

city: Ferrara

first: Cristian

last: Bassi

state: Ferrara

address: Via Fossato di Mortara 70

department: Medicina Traslazionale e per la Romagna

country: Italy

institute: Università di Ferrara

data_processing:
Raw base-call data have been demultiplexed and converted to FASTQ format using Illumina BaseSpace Sequence Hub.
Quality check has been performed using FastQC tool.
Online Qiagen GeneGlobe Data Analysis Center has been usded to perform micro-RNA mapping and counts.
Raw counts obtained from Qiagen GeneGlobe Data Analysis Center have been further normalized and differentially expressed genes have been identified using DESeq2 bioconductor package.
Differentially expressed miRNAs with a pValue ≤ 0.05 and a FC ≤ −1.5 or ≥ 1.5 were considered statistically significant.
Assembly: miRBase v.22
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Normal skin

growth_protocol: Differential trypsinization was employed to separate fibroblasts and keratinocytes from keratinocytes colonies. Fibroblasts were cultured on 6-well plates using media DMEM:F12; 5% FBS; 1% Pen/Strep. Keratinocytes isolated from the colonies were transferred to 6-well plates and cultured DKSFM media.

extract_protocol:
Total RNA, including miRNA, was isolated from primary human cell samples using miRNeasy minikit Qiagen (Cat.# 217004, QIAGEN) according to the manufacturer’s instructions.
miRNAs libraries were prepaired  using QIAseq miRNA Library kit (Cat.331505 Qiagen), starting from 100 ng of total RNA

value: Normal skin

value: fibroblasts


title: Normali skin fibroblasts - Sample19 [S19]


title: 3543_OF1A_1-6-I1-M23

value: nuclear RNA + genomic DNA


title: Feces_DR_wild_mouse_community_with_Bifidobacteria_rep1


title: 3543_OF1A_1-6-I1-M12


title: Normali skin fibroblasts - Sample18 [S18]


title: Feces_AD_wild_mouse_community_with_Bifidobacteria_rep5

value: ad libitum


title: Feces_AD_wild_mouse_community_with_Bifidobacteria_rep4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026566LR01-GA4-1-8-30]

description: Carbon tetrachloride, 2 ml/kg, Day 5, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026565LR01-GA3-3-8-30]

description: Carbon tetrachloride, 1.5 ml/kg, Day 5, Repeat 3


title: 3543_OF1A_1-6-I1-N11


title: Feces_DR_wild_mouse_community_with_Bifidobacteria_rep3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026563LR01-GA3-1-8-30]

description: Carbon tetrachloride, 1.5 ml/kg, Day 5, Repeat 1


title: VLS fibroblasts - Sample15 [S15]

source_name: vulvar lichen sclerosus (VLS)

value: vulvar lichen sclerosus (VLS)


title: 3543_OF1A_1-6-I1-M11


title: Scr control, rep1

description:
Control_1
Sample is a pooled result of raw files of pool 1 (p1) and pool 2 (p2)

value: Melanoma cell line

value: Scr control


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026564LR01-GA3-2-8-30]

description: Carbon tetrachloride, 1.5 ml/kg, Day 5, Repeat 2

value: 8 wks


title: Normali skin fibroblasts - Sample17 [S17]


title: Feces_AD_wild_mouse_community_with_Bifidobacteria_rep3


title: 3543_OF1A_1-6-I1-L11


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026562LR01-GA2-3-8-30]

description: Carbon tetrachloride, 1 ml/kg, Day 5, Repeat 3


title: VLS fibroblasts - Sample14 [S14]


title: 3543_OF1A_1-6-I1-K24


title: Feces_AD_wild_mouse_community_with_Bifidobacteria_rep1


title: Feces_AD_wild_mouse_community_with_Bifidobacteria_rep2


title: VLS fibroblasts - Sample13 [S13]


title: Feces_DR_wild_mouse_community_no_Bifidobacteria_rep4

value: wild mouse community without Bifidobacteria


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026561LR01-GA2-2-8-30]

description: Carbon tetrachloride, 1 ml/kg, Day 5, Repeat 2


title: Feces_DR_wild_mouse_community_no_Bifidobacteria_rep3

value: dietary restriction


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026560LR01-GA2-1-8-30]

description: Carbon tetrachloride, 1 ml/kg, Day 5, Repeat 1


title: VLS fibroblasts - Sample12 [S12]


title: VLS fibroblasts - Sample11 [S11]


title: 3543_OF1A_1-6-I1-K12


title: 3543_OF1A_1-6-I1-L23


title: 3543_OF1A_1-6-I1-K23


title: Feces_DR_wild_mouse_community_no_Bifidobacteria_rep2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026559LR01-GA1-3-8-30]

description: Carbon tetrachloride, 0.5 ml/kg, Day 5, Repeat 3


title: Normali skin fibroblasts - Sample16 [S16]


title: Normali skin keratinocytes - Sample9 [S10]

value: keratinocytes


title: Feces_DR_wild_mouse_community_no_Bifidobacteria_rep1

value: feces


title: 3543_OF1A_1-6-I1-J24


title: 3543_OF1A_1-6-I1-K11


title: 3543_OF1A_1-6-I1-L12


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026557LR01-GA1-1-8-30]

description: Carbon tetrachloride, 0.5 ml/kg, Day 5, Repeat 1

value: male


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026558LR01-GA1-2-8-30]

description: Carbon tetrachloride, 0.5 ml/kg, Day 5, Repeat 2

value: whole blood


title: Feces_AD_wild_mouse_community_no_Bifidobacteria_rep4


title: 3543_OF1A_1-6-I1-J23


title: Normali skin keratinocytes - Sample8 [S8]


title: Normali skin keratinocytes - Sample7 [S7]


title: Feces_AD_wild_mouse_community_no_Bifidobacteria_rep2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026556LR01-1-3-8-30]

description: Sodium chloride, 0.9%, Day 5, Repeat 3

value: Sodium chloride, 0.9%, Day 5, Repeat 3


title: Feces_AD_wild_mouse_community_no_Bifidobacteria_rep3


title: 3543_OF1A_1-6-I1-J11

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Normali skin keratinocytes - Sample6 [S6]


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026555LR01-1-2-8-30]

description: Sodium chloride, 0.9%, Day 5, Repeat 2

value: Sodium chloride, 0.9%, Day 5, Repeat 2


title: VLS keratinocytes - Sample5 [S5]


title: 3543_OF1A_1-6-I1-J12

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026554LR01-1-1-8-30]

description: Sodium chloride, 0.9%, Day 5, Repeat 1

value: Sodium chloride, 0.9%, Day 5, Repeat 1


title: VLS keratinocytes - Sample4 [S4]


title: 3543_OF1A_1-6-I1-I23

value: nuclear RNA + genomic DNA


title: PBMCs, Galectin-8, 24 h, 3

city: Shanghai

first: Yiting

last: Wang

address: Dongfang Road 1630

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

data_processing:
CLC Genomics Workbench v 11.0.1
The raw data from sequencing are quality assessed by FastQC and trimmed by Trimmomatic to obtain relatively accurate and valid data.
Trimmed sequence reads were compared to the reference genome using HISAT2.
Read count extraction and normalization were performed using StringTie and known gene models.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: PBMCs

growth_protocol: Human PBMCs were cultured in AIM-V medium with antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). The mRNA was quantified using the Qubit RNA Detection Kit and enriched by Oligo(dT) magnetic beads  for the construction of sequencing libraries.
ctDNA was synthesized with commercial Strand Synthesis Reaction Buffer and then purified with Hieff NGS™ DNA Selection Beads. The products are sequentially subjected to end repair/dA tail addition, splice ligation, as well as purification and fragment size sorting before being amplified to build the library.

treatment_protocol: Experiment group were treated with 4 ug/ml of Galectin-8 for 24 hours.

value: PBMCs

value: WT

tag: time


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026553LR01-GC4-1-8-29]

description: Valproate, 1000 mg/kg, Day 4, Repeat 1

value: Valproate, 1000 mg/kg, Day 4, Repeat 1


title: VLS keratinocytes - Sample3 [S3]

value: vulvar lichen sclerosus (VLS)


title: 3543_OF1A_1-6-I1-I12


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026552LR01-GC2-2-8-29]

description: Valproate, 500 mg/kg, Day 4, Repeat 2

value: 8 wks

value: Valproate, 500 mg/kg, Day 4, Repeat 2


title: VLS keratinocytes - Sample2 [S2]


title: PBMCs, Galectin-8, 24 h, 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026551LR01-GC2-1-8-29]

description: Valproate, 500 mg/kg, Day 4, Repeat 1

value: Valproate, 500 mg/kg, Day 4, Repeat 1


title: VLS keratinocytes - Sample1 [S1]

value: keratinocytes


title: 3543_OF1A_1-6-I1-I11


title: PBMCs, PBS, 24 h, 3

value: PBS


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026550LR01-GC1-3-8-29]

description: Valproate, 250 mg/kg, Day 4, Repeat 3

value: male

value: Valproate, 250 mg/kg, Day 4, Repeat 3


title: 3543_OF1A_1-6-I1-H23


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026548LR01-GC1-1-8-29]

description: Valproate, 250 mg/kg, Day 4, Repeat 1

value: whole blood

value: Valproate, 250 mg/kg, Day 4, Repeat 1


title: 3543_OF1A_1-6-I1-H12

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: PBMCs, PBS, 24 h, 1


title: PBMCs, PBS, 24 h, 2


title: Feces_AD_wild_mouse_community_no_Bifidobacteria_rep1

value: ad libitum

value: wild mouse community without Bifidobacteria

value: feces


title: 3543_OF1A_1-6-I1-I24

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-6-I1-H11


title: CD14+ monocytes, Galectin-8, Day 3 rep3

source_name: CD14+ monocytes

growth_protocol: CD14+ monocytes were isolated from human PBMC and cultured in AIM-V medium with antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Experiment group were treated with 4 ug/ml of Galectin-8 for 3 days in the presence of GM-CSF (Stem Cell).

value: CD14+ monocytes

value: WT

value: Day 3


title: PGF2a, 48h, biol rep 3

city: Coventry

first: Richard

middle: Jan

last: Stark

address: Gibbet Hill Campus, The University of Warwick

department: Bioinformatics RTP

country: United Kingdom

institute: University of Warwick

data_processing:
Demultiplexing, Bcl2fastq, v2.20.0.422
Read quality assessment, FastQC, v0.11.9
Mapping, STAR, v2.7.9a
Read counting, FeatureCounts, v2.0.1
Assembly: GRCh38 release 86
Supplementary files format and content: Tab delimited text file with raw read counts. One file per sample.

source_name: myometrium

growth_protocol: MYLA cells were seeded into T75 cm2 flasks and allowed to grow to 95-100% confluency.

extract_protocol:
RNA was extracted from pelleted cells using a Gen EluteTM Total RNA Purification kit (Sigma Aldrich, Poole, UK) according to the manufacturer’s instructions. RNA concentration and purity were determined using a Nanodrop ND-1000 (ThermoFisher Scientific, Loughborough, UK). All RNA samples were stored at -80°C until use.
cDNA was generated using a Vilo cDNA Synthesis Kit (Invitrogen, Paisley, UK) according to manufactures instructions and using a VeritiTM 96-well Fast Thermal Cycler (ThermoFisher, Loughborough, UK).

treatment_protocol: Cells were serum starved for 24 hours then treated with either; 1 μM PGF2α, PGF2α vehicle (ethanol) equivalent, or 1 μM PGF2α + 1 μM FP antagonist at time (T) 0. Cells were harvested at T=1, 3, 6, 9, 12, 24 and 48 hours, pelleted (1200 rpm, 5 minutes, 4°C) and snap frozen on dry ice before storage at -80°C.

value: myometrium

value: immortalised myometrial cells (MYLA)

value: cell line

value: immortalised uterine smooth muscle cell line

tag: identifier


title: 3543_OF1A_1-6-I1-G24


title: PGF2a, 48h, biol rep 1


title: PGF2a, 48h, biol rep 2


title: PGF2a, 24h, biol rep 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026547LR01-GA4-3-8-29]

description: Carbon tetrachloride, 2 ml/kg, Day 4, Repeat 3

value: 8 wks

value: male


title: PBMCs, Galectin-8, 24 h, 2

value: PBMCs


title: CD14+ monocytes, Galectin-8, Day 3 rep2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026546LR01-GA4-2-8-29]

description: Carbon tetrachloride, 2 ml/kg, Day 4, Repeat 2

value: whole blood


title: 3543_OF1A_1-6-I1-G23

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: CD14+ monocytes, Galectin-8, Day 3 rep1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026545LR01-GA4-1-8-29]

description: Carbon tetrachloride, 2 ml/kg, Day 4, Repeat 1


title: PGF2a, 24h, biol rep 2


title: 3543_OF1A_1-6-I1-G12


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026544LR01-GA3-3-8-29]

description: Carbon tetrachloride, 1.5 ml/kg, Day 4, Repeat 3


title: CD14+ monocytes, PBS, Day 3 rep3

value: PBS


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026549LR01-GC1-2-8-29]

description: Valproate, 250 mg/kg, Day 4, Repeat 2

value: Valproate, 250 mg/kg, Day 4, Repeat 2


title: PGF2a, 12h, biol rep 3


title: PGF2a, 24h, biol rep 1


title: CD14+ monocytes, PBS, Day 3 rep2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026543LR01-GA3-2-8-29]

description: Carbon tetrachloride, 1.5 ml/kg, Day 4, Repeat 2


title: 3543_OF1A_1-6-I1-G11


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026542LR01-GA3-1-8-29]

description: Carbon tetrachloride, 1.5 ml/kg, Day 4, Repeat 1


title: CD14+ monocytes, PBS, Day 3 rep1


title: PGF2a, 12h, biol rep 2


title: PGF2a, 12h, biol rep 1


title: 3543_OF1A_1-6-I1-F24


title: 3543_OF1A_1-6-I1-F23


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026541LR01-GA2-3-8-29]

description: Carbon tetrachloride, 1 ml/kg, Day 4, Repeat 3


title: 3543_OF1A_1-6-I1-F12


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026540LR01-GA2-2-8-29]

description: Carbon tetrachloride, 1 ml/kg, Day 4, Repeat 2


title: 3543_OF1A_1-6-I1-F11


title: Sham-WT [Sham83]

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
QC and trimming of raw reads using fastp v0.20
Pseudo-alignment of trimmed reads and gene quantification using Kallisto v0.46.1
Differential gene expression analysis using R package DESeq2 v1.38
Over-representation analysis of DEGs using R package clusterProfiler v4.6.0
Assembly: build GRCm39 (GENCODE release M31)

source_name: Liver

extract_protocol:
Total RNA was extracted from liver tissues using the Qiagen RNeasy Plus Mini Kit
Samples with RIN > 7 were used in mRNA-seq library generation using the NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit. Briefly, 200 ng total RNA were used as input. RNA fragmentation was set at 10 minutes and 12 PCR cycles were used in final library generation. Library quantification and characterization were assessed with Agilent BioAnalyzer HS DNA Kit.

value: Liver

tag: condition

value: Empty scaffold transplant


title: Sham-WT [Sham80]


title: Sham-WT [Sham79]


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026539LR01-GA2-1-8-29]

description: Carbon tetrachloride, 1 ml/kg, Day 4, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026538LR01-GA1-3-8-29]

description: Carbon tetrachloride, 0.5 ml/kg, Day 4, Repeat 3


title: Control, 48h, biol rep 3

value: control


title: 3543_OF1A_1-6-I1-E23

value: Female

value: nuclear RNA + genomic DNA


title: Sham-WT [Sham52]


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026537LR01-GA1-2-8-29]

description: Carbon tetrachloride, 0.5 ml/kg, Day 4, Repeat 2


title: Sham-WT [Sham179]


title: 3543_OF1A_1-6-I1-E12


title: Control, 48h, biol rep 1


title: Sham-WT [Sham178]


title: Control, 48h, biol rep 2


title: Sham-WT [Sham176]


title: 3543_OF1A_1-6-I1-E11


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026535LR01-1-3-8-29]

description: Sodium chloride, 0.9%, Day 4, Repeat 3

value: Sodium chloride, 0.9%, Day 4, Repeat 3


title: Control, 24h, biol rep 2

value: myometrium


title: Sham-WT [Sham175]


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026534LR01-1-2-8-29]

description: Sodium chloride, 0.9%, Day 4, Repeat 2

value: Sodium chloride, 0.9%, Day 4, Repeat 2


title: PGF2a, 9h, biol rep 2

value: immortalised myometrial cells (MYLA)

value: cell line


title: PGF2a, 9h, biol rep 3

value: immortalised uterine smooth muscle cell line


title: 3543_OF1A_1-6-I1-D24


title: iBAT 2x [iBAT90]

value: BAT pre-adipocyte transplant


title: 3543_OF1A_1-6-I1-E24


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026533LR01-1-1-8-29]

description: Sodium chloride, 0.9%, Day 4, Repeat 1

value: 8 wks

value: male

value: Sodium chloride, 0.9%, Day 4, Repeat 1


title: iBAT 2x [iBAT89]


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026532LR01-GC4-3-8-28]

description: Valproate, 2000 mg/kg, Day 3, Repeat 3

value: whole blood

value: Valproate, 2000 mg/kg, Day 3, Repeat 3


title: 3543_OF1A_1-6-I1-D12

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-6-I1-D11


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026536LR01-GA1-1-8-29]

description: Carbon tetrachloride, 0.5 ml/kg, Day 4, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026531LR01-GC4-2-8-28]

description: Valproate, 2000 mg/kg, Day 3, Repeat 2

value: Valproate, 2000 mg/kg, Day 3, Repeat 2


title: iBAT 2x [iBAT88]

value: Liver


title: Control, 12h, biol rep 2

value: control


title: iBAT 2x [iBAT130]


title: Control, 12h, biol rep 1


title: Control, 24h, biol rep 3


title: Control, 24h, biol rep 1


title: 3543_OF1A_1-6-I1-D23

value: Female

value: nuclear RNA + genomic DNA


title: Control, 9h, biol rep 3

value: myometrium


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026529LR01-GC3-3-8-28]

description: Valproate, 1000 mg/kg, Day 3, Repeat 3

value: Valproate, 1000 mg/kg, Day 3, Repeat 3


title: 3543_OF1A_1-6-I1-C23


title: 3543_OF1A_1-6-I1-C12


title: PGF2a, 9h, biol rep 1

value: immortalised myometrial cells (MYLA)


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026528LR01-GC3-2-8-28]

description: Valproate, 1000 mg/kg, Day 3, Repeat 2

value: Valproate, 1000 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_1-6-I1-C11


title: iBAT 2x [iBAT129]


title: PGF2a, 6h, biol rep 3

value: cell line

value: immortalised uterine smooth muscle cell line


title: Control, 12h, biol rep 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026527LR01-GC3-1-8-28]

description: Valproate, 1000 mg/kg, Day 3, Repeat 1

value: 8 wks

value: Valproate, 1000 mg/kg, Day 3, Repeat 1


title: 3543_OF1A_1-6-I1-B24


title: PGF2a, 6h, biol rep 2


title: 3543_OF1A_1-6-I1-B23


title: Liver, HKO-3, HFD, 12wks

city: Nanjing

first: ying

last: zheng

address: 639 Longmian Avenue, Chunhua Street, Jiangning District,

institute: China Pharmaceutical University

description: hepatocyte-specific G3bp1-knockout

data_processing:
CLC Genomics Workbench V11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length faction: 0.8 similarity faction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

growth_protocol: 6-week-old G3bp1-Flox and G3bp1-HKO mice were fed a high-fat diet for 12 weeks.

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen). 1.3μg total RNA was used for the construction of suquencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufaturer's protocols.

treatment_protocol: Mouse liver tissues, rapidly frozen in liquid nitrogen, were stored at -80°C for subsequent RNA extraction

value: liver

value: hepatocyte-specific G3bp1-knockout

value: HFD-diet


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026526LR01-GC2-3-8-28]

description: Valproate, 500 mg/kg, Day 3, Repeat 3

value: male

value: whole blood

value: Valproate, 500 mg/kg, Day 3, Repeat 3


title: 3543_OF1A_1-6-I1-C24

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Liver, HKO-2, HFD, 12wks

description: hepatocyte-specific G3bp1-knockout


title: PGF2a, 6h, biol rep 1


title: Liver, HKO-1, HFD, 12wks

description: hepatocyte-specific G3bp1-knockout


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026530LR01-GC4-1-8-28]

description: Valproate, 2000 mg/kg, Day 3, Repeat 1

value: Valproate, 2000 mg/kg, Day 3, Repeat 1


title: Liver, Flox-3, HFD, 12wks

description: Litter control

source_name: Liver, litter control

value: Flox


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026525LR01-GC2-2-8-28]

description: Valproate, 500 mg/kg, Day 3, Repeat 2

value: Valproate, 500 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_1-6-I1-B12

value: Female

value: nuclear RNA + genomic DNA


title: PGF2a, 3h, biol rep 3

value: myometrium

value: immortalised myometrial cells (MYLA)


title: 3543_OF1A_1-6-I1-B11


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026524LR01-GC2-1-8-28]

description: Valproate, 500 mg/kg, Day 3, Repeat 1

value: Valproate, 500 mg/kg, Day 3, Repeat 1


title: iBAT 2x [iBAT115]

value: Liver

value: BAT pre-adipocyte transplant


title: Liver, Flox-2, HFD, 12wks

description: Litter control

value: liver


title: PGF2a, 3h, biol rep 1

value: cell line

value: immortalised uterine smooth muscle cell line


title: 3543_OF1A_1-6-I1-A24


title: Liver, Flox-1, HFD, 12wks

description: Litter control

value: HFD-diet


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026523LR01-GC1-3-8-28]

description: Valproate, 250 mg/kg, Day 3, Repeat 3

value: 8 wks

value: male

value: whole blood

value: Valproate, 250 mg/kg, Day 3, Repeat 3


title: PGF2a, 3h, biol rep 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026521LR01GC1-1-8-28]

description: Valproate, 250 mg/kg, Day 3, Repeat 1

value: Valproate, 250 mg/kg, Day 3, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026522LR01-GC1-2-8-28]

description: Valproate, 250 mg/kg, Day 3, Repeat 2

value: Valproate, 250 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_1-6-I1-A23

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: PGF2a, 1h, biol rep 2

value: myometrium


title: PGF2a, 1h, biol rep 3

value: immortalised myometrial cells (MYLA)


title: 3543_OF1A_1-6-I1-A12

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-6-I1-A11


title: iM-Piezo1KO_Day 28_1

city: Chuo-ku, Kobe City, Hyogo

first: Yu

last: Hirata

address: 7-5-1 Kusunoki-cho

department: Department of Internal Medicine Division of Diabetes and Endocrinology

country: Japan

institute: Kobe University Graduate School of Medicine

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCm38 (mm10) whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCm38 (mm10)
Supplementary files format and content: The excel file includes read counts for each sample.

source_name: gastrocnemius muscle

growth_protocol: Mice were maintained on a 12-hour light/dark cycle and allowed free access to food and water.

extract_protocol:
Total RNA was extracted from the cells with the use of an RNeasy Mini Kit (Qiagen) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The anesthetized mice were subjected to hindlimb cast-immobilization with plastic tubes and adhesive tape for 3 or 10 days.

value: muscle

value: tamoxifen-inducible skeletal muscle-specific Piezo1 KO

value: iM-Piezo1KO_Day 28


title: iM-Piezo1KO_Day 28_2


title: PGF2a, 1h, biol rep 1

value: cell line


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026519LR01GB4-2-8-28]

description: Isoniazid, 3200 mg/kg, Day 3, Repeat 2

value: Isoniazid, 3200 mg/kg, Day 3, Repeat 2


title: WT_Day 28_2

value: wild type

value: WT_Day 28


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026520LR01GB4-3-8-28]

description: Isoniazid, 3200 mg/kg, Day 3, Repeat 3

value: 8 wks

value: male

value: Isoniazid, 3200 mg/kg, Day 3, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026518LR01GB4-1-8-28]

description: Isoniazid, 3200 mg/kg, Day 3, Repeat 1

value: whole blood

value: Isoniazid, 3200 mg/kg, Day 3, Repeat 1


title: 3543_OF1A_1-5-I1-P9

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: WT_Day 28_1


title: Control, 9h, biol rep 1

value: immortalised uterine smooth muscle cell line

value: control


title: 3543_OF1A_1-5-I1-P21

value: Female


title: iM-Piezo1KO_Day 14_3

value: iM-Piezo1KO_Day 14


title: Control, 6h, biol rep 3

value: myometrium

value: immortalised myometrial cells (MYLA)


title: 3543_OF1A_1-5-I1-P10

value: nuclear RNA + genomic DNA


title: iM-Piezo1KO_Day 14_2

value: muscle

value: tamoxifen-inducible skeletal muscle-specific Piezo1 KO


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026516LR01GB3-2-8-28]

description: Isoniazid, 1600 mg/kg, Day 3, Repeat 2

value: Isoniazid, 1600 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_1-5-I1-O9


title: iM-Piezo1KO_Day 14_1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026515LR01GB3-1-8-28]

description: Isoniazid, 1600 mg/kg, Day 3, Repeat 1

value: Isoniazid, 1600 mg/kg, Day 3, Repeat 1


title: Control, 6h, biol rep 1

value: cell line


title: Control, 6h, biol rep 2


title: WT_Day 14_3

value: wild type

value: WT_Day 14


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026514LR01GB2-3-8-28]

description: Isoniazid, 800 mg/kg, Day 3, Repeat 3

value: 8 wks

value: male

value: whole blood

value: Isoniazid, 800 mg/kg, Day 3, Repeat 3


title: 3543_OF1A_1-5-I1-O21

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: WT_Day 14_2


title: 3543_OF1A_1-5-I1-O22

value: Female


title: Control, 3h, biol rep 3

value: immortalised uterine smooth muscle cell line

value: control


title: WT_Day 14_1


title: Control, 9h, biol rep 2

value: myometrium

value: immortalised myometrial cells (MYLA)


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026512LR01-GB2-1-8-28]

description: Isoniazid, 800 mg/kg, Day 3, Repeat 1

value: Isoniazid, 800 mg/kg, Day 3, Repeat 1


title: iM-Piezo1KO_Day 3_3

value: muscle

value: tamoxifen-inducible skeletal muscle-specific Piezo1 KO

value: iM-Piezo1KO_Day 3


title: 3543_OF1A_1-5-I1-N9

value: nuclear RNA + genomic DNA


title: Control, 3h, biol rep 2

value: cell line


title: 3543_OF1A_1-5-I1-O10


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026517LR01GB3-3-8-28]

description: Isoniazid, 1600 mg/kg, Day 3, Repeat 3

value: Isoniazid, 1600 mg/kg, Day 3, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026513LR01GB2-2-8-28]

description: Isoniazid, 800 mg/kg, Day 3, Repeat 2

value: 8 wks

value: Isoniazid, 800 mg/kg, Day 3, Repeat 2


title: iM-Piezo1KO_Day 3_2


title: 3543_OF1A_1-5-I1-N22


title: Control, 1h, biol rep 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026511LR01GB1-3-8-28]

description: Isoniazid, 400 mg/kg, Day 3, Repeat 3

value: male

value: whole blood

value: Isoniazid, 400 mg/kg, Day 3, Repeat 3


title: 3543_OF1A_1-5-I1-N21

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Control, 1h, biol rep 2

value: immortalised uterine smooth muscle cell line

value: control


title: iM-Piezo1KO_Day 3_1


title: 3543_OF1A_1-5-I1-N10


title: WT_Day 3_3

value: wild type

value: WT_Day 3


title: 3543_OF1A_1-5-I1-M9


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026508LR01GA4-3-8-28]

description: Carbon tetrachloride, 2 ml/kg, Day 3, Repeat 3


title: WT_Day 3_2

value: muscle


title: Control, 1h, biol rep 1

value: myometrium

value: immortalised myometrial cells (MYLA)


title: Control, 3h, biol rep 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026509LR01GB1-1-8-28]

description: Isoniazid, 400 mg/kg, Day 3, Repeat 1

value: Isoniazid, 400 mg/kg, Day 3, Repeat 1


title: 3543_OF1A_1-5-I1-M22

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026507LR01GA4-2-8-28]

description: Carbon tetrachloride, 2 ml/kg, Day 3, Repeat 2


title: S08, 5hmC_NEIL2_KO, rep 4

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

data_processing:
The clean reads were aligned to reference human genome hg37 by BWA. Sam filles were sorted as bam files and indexed by samtools.
The processing data of 5mC and 5hmC count in CpG context were extract using MethylDackel tool in default setting.
The processing data was further used to identify the differentially methylation regions with methylKit.
Assembly: hg37
Supplementary files format and content: The 5mC and 5hmC count data are in bedGraph format. The data consists of 6 columns in the order as: 1.The chromosome name; 2.The start coordinate; 3.The end coordinate; 4.The unmethylation percentage ; 5.The number of  unmethylated C; 6. The number of methylated C.
Library strategy: TAPS-seq and CAPS-seq

extract_protocol:
DNA extracted by NAxtra magnetic nanoparticles.
DNA libraries for genome sequencing of 5mC and 5hmC were prepared using TAPS and CAPS protocols (Liu Y., etal, Nature Communications 2021).


title: S07, 5hmC_NEIL2_KO, rep 3


title: WT_Day 3_1


title: S06, 5hmC_NEIL2_KO, rep 2


title: IM_Day 10 + Ab_3

value: IM_Day 10 + neutralizing antibodies to CXCL10


title: 3543_OF1A_1-5-I1-M21


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026505LR01GA3-3-8-28]

description: Carbon tetrachloride, 1.5 ml/kg, Day 3, Repeat 3

value: 8 wks


title: S05, 5hmC_NEIL2_KO, rep 1


title: 3543_OF1A_1-5-I1-M10


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026510LR01GB1-2-8-28]

description: Isoniazid, 400 mg/kg, Day 3, Repeat 2

value: Isoniazid, 400 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_1-5-I1-L9


title: IM_Day 10 + Ab_2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026503LR01GA3-1-8-28]

description: Carbon tetrachloride, 1.5 ml/kg, Day 3, Repeat 1

value: male


title: S04, 5hmC_WT, rep 4

value: WT


title: IM_Day 10 + Ab_1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026504LR01GA3-2-8-28]

description: Carbon tetrachloride, 1.5 ml/kg, Day 3, Repeat 2

value: whole blood


title: 3543_OF1A_1-5-I1-L22

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: S03, 5hmC_WT, rep 3


title: IM_Day 10_3

value: IM_Day 10


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026502LR01GA2-3-8-28]

description: Carbon tetrachloride, 1 ml/kg, Day 3, Repeat 3


title: 3543_OF1A_1-5-I1-L21

value: Female


title: S02, 5hmC_WT, rep 2


title: IM_Day 10_2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026501LR01GA2-2-8-28]

description: Carbon tetrachloride, 1 ml/kg, Day 3, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026506LR01GA4-1-8-28]

description: Carbon tetrachloride, 2 ml/kg, Day 3, Repeat 1


title: S01, 5hmC_WT, rep 1


title: IM_Day 10_1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026500LR01GA2-1-8-28]

description: Carbon tetrachloride, 1 ml/kg, Day 3, Repeat 1


title: 3543_OF1A_1-5-I1-K9


title: S08, 5mC_NEIL2_KO, rep 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026499LR01GA1-3-8-28]

description: Carbon tetrachloride, 0.5 ml/kg, Day 3, Repeat 3


title: Control_Day 10_3

value: Control_Day 10


title: Control_Day 10_2

value: wild type


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026498LR01GA1-2-8-28]

description: Carbon tetrachloride, 0.5 ml/kg, Day 3, Repeat 2


title: S07, 5mC_NEIL2_KO, rep 3


title: 3543_OF1A_1-5-I1-K21


title: 3543_OF1A_1-5-I1-K22


title: Control_Day 10_1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026497LR01GA1-1-8-28]

description: Carbon tetrachloride, 0.5 ml/kg, Day 3, Repeat 1


title: 3543_OF1A_1-5-I1-K10


title: IM_Day 3 + Ab_3

value: IM_Day 3 + neutralizing antibodies to CXCL10


title: S05, 5mC_NEIL2_KO, rep 1


title: IM_Day 3 + Ab_2

value: muscle


title: S04, 5mC_WT, rep 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026496LR011-3-8-28]

description: Sodium chloride, 0.9%, Day 3, Repeat 3

value: Sodium chloride, 0.9%, Day 3, Repeat 3


title: 3543_OF1A_1-5-I1-L10


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026495LR011-2-8-28]

description: Sodium chloride, 0.9%, Day 3, Repeat 2

value: Sodium chloride, 0.9%, Day 3, Repeat 2


title: IM_Day 3 + Ab_1


title: 3543_OF1A_1-5-I1-J22


title: S03, 5mC_WT, rep 3


title: 3543_OF1A_1-5-I1-J21


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026494LR011-1-8-28]

description: Sodium chloride, 0.9%, Day 3, Repeat 1

value: Sodium chloride, 0.9%, Day 3, Repeat 1


title: IM_Day 3_3

value: IM_Day 3


title: S02, 5mC_WT, rep 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026493LR01GC4-3-8-26]

description: Valproate, 2000 mg/kg, Day 2, Repeat 3

value: Valproate, 2000 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_1-5-I1-J10

value: nuclear RNA + genomic DNA


title: S06, 5mC_NEIL2_KO, rep 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026492LR01GC4-2-8-26]

description: Valproate, 2000 mg/kg, Day 2, Repeat 2

value: 8 wks

value: Valproate, 2000 mg/kg, Day 2, Repeat 2


title: 3543_OF1A_1-5-I1-I9


title: IM_Day 3_2


title: 3543_OF1A_1-5-I1-J9


title: IM_Day 3_1


title: FDCs, Ngfr KO, 3

city: Madrid

first: Alberto

last: Hernández-Barracno

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: Spanish National Cancer Research Center

data_processing:
RTA v1.18.66.3
FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).
Sequencing reads were aligned to the mouse reference transcriptome (mm10 v90) and quantified with RSem v1.3.1
Raw counts were normalized with TPM (Transcripts per million) and TMM (Trimmed mean of M-values) methods, transformed into log2 expression (log2(rawCount+1)) and compared to calculate fold-change and corrected p-value (FDR) using a Benjamini and Hochberg procedure.
Only those genes expressed with at least 1 count in a number of samples equal to the number of replicate samples of the condition with less replicates were taken into account.
Assembly: mm10 v90
Supplementary files format and content: Tab-delimited text file include TMM values for each sample

source_name: Lymph node

extract_protocol:
cDNA was amplified from the collected cells using the SMART-Seq v4 Ultra Low Input RNA Kit (TakaraBio).
1ng of amplified cDNA was used to generate barcoded libraries with the Nextera XT DNA library preparation kit (Illumina). The size of the libraries was checked using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip and their [EMG1] concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific).

treatment_protocol:
Non-immunized male mice from 8 to 12 weeks of age were used to sample popliteal lymph nodes
FACS isolated cells were collected into lysis buffer (TakaraBio) containing recombinant RNase Inhibitor (TakaraBio)

value: Lymph node

value: Follicualr dendritic cells

value: Ngfr KO


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026491LR01GC4-1-8-26]

description: Valproate, 2000 mg/kg, Day 2, Repeat 1

value: male

value: whole blood

value: Valproate, 2000 mg/kg, Day 2, Repeat 1


title: Control_Day 3_3

value: wild type

value: Control_Day 3


title: FDCs, Ngfr KO, 1


title: 3543_OF1A_1-5-I1-I21

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026490LR01GC3-3-8-26]

description: Valproate, 1000 mg/kg, Day 2, Repeat 3

value: Valproate, 1000 mg/kg, Day 2, Repeat 3


title: Control_Day 3_2

value: muscle


title: FDCs, Ngfr KO, 2


title: FDCs, WT, 4

value: WT


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026489LR01GC3-2-8-26]

description: Valproate, 1000 mg/kg, Day 2, Repeat 2

value: Valproate, 1000 mg/kg, Day 2, Repeat 2


title: Control_Day 3_1


title: 3543_OF1A_1-5-I1-I10

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026488LR01GC3-1-8-26]

description: Valproate, 1000 mg/kg, Day 2, Repeat 1

value: 8 wks

value: Valproate, 1000 mg/kg, Day 2, Repeat 1


title: 3543_OF1A_1-5-I1-I22


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026487LR01GC2-3-8-26]

description: Valproate, 500 mg/kg, Day 2, Repeat 3

value: Valproate, 500 mg/kg, Day 2, Repeat 3


title: S01, 5mC_WT, rep 1


title: FDCs, WT, 2

value: Lymph node

value: Follicualr dendritic cells


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026486LR01GC2-2-8-26]

description: Valproate, 500 mg/kg, Day 2, Repeat 2

value: male

value: Valproate, 500 mg/kg, Day 2, Repeat 2


title: iTregs IP(H3R2me2s)

city: Amherst

first: Nidhi

last: Jadon

state: MA

address: 661 N plesant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts Amherst

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of [mus musculus] using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis. MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis. The differentially binding peaks were identified by a python script，using fisher test. The Homer（version 4.10）was used for motifs analysis.
Assembly: mm10
Supplementary files format and content: Analysis Step Software Version Description Parameter
Supplementary files format and content: Raw data quality control FastQC version v0.11.5 Generate NGS quality control report Default Parameter
Supplementary files format and content: citation:
Supplementary files format and content: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Supplementary files format and content: Raw data clean Trimmomatic version 0.36 Filter out the adaptor and low quality reads ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE
Supplementary files format and content: citation:
Supplementary files format and content: Trimmomatic: A flexible read trimming tool for Illumina NGS data
Supplementary files format and content: http://www.usadellab.org/cms/index.php?page=trimmomatic
Supplementary files format and content: Clean data mapping STAR version 2.5.3a mapping the reads to the genome --outSAMtype BAM SortedByCoordinate
Supplementary files format and content: citation:
Supplementary files format and content: STAR: ultrafast universal RNA-seq aligner
Supplementary files format and content: Mapped reads evaluation RSeQC version 2.6 Evaluate mapped reads distribution, coverage uniformity, strand specificity, etc. Default Parameter
Supplementary files format and content: citation:
Supplementary files format and content: RSeQC: An RNA-seq Quality Control Package
Supplementary files format and content: call peak MACS2  Version  Gives robust and Transcript factors: macs2 callpeak -t {ip_bams} -c {input_bams} -g {GENOME_SIZE} -n {wildcards.sample} --outdir f BAM -B --bw 300 --mfold 5 50 --slocal=1000 --llocal=10000 --keep-dup=1 -p 0.01
Supplementary files format and content: high resolution ChIP-Seq peak predictions Histons: epic --treatment {ip_beds} --control {input_beds} --number-cores {threads} --outfile {output} --bed {bbeedd} --chromsizes {genome_size} --false-discovery-rate-cutoff 0.00001 --effective-genome-fraction 1 --log {log_file}
Supplementary files format and content: Peak annotation and peak distribution bedtools Version v2.25.0 annotate the peak related genes intersectBed -a ｛peak.bed｝ -b {genome.bed} -wa -wb > {out.bed}
Supplementary files format and content: citation:
Supplementary files format and content: bedtools: a powerful toolset for genome arithmetic
Supplementary files format and content: motif homer Version v4.10 motif search findMotifsGenome.pl {peak_file} {genome.fa} {out_dir}
Supplementary files format and content: citation:
Supplementary files format and content: Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432
Supplementary files format and content: Network analysis igraph(R pacakge) Version Network analysis Default parameters
Supplementary files format and content: 1.0.0  https://igraph.org/
Supplementary files format and content: IGraph/M: a Mathematicainterface forigraph

source_name: iTregs

growth_protocol: CD4 T cells were extracted from spleen of C57BL\6 mice, Cells were given polarizing cytokines and DMEM+RPMI media supplemented with FBS. Cells were kept in 7% CO2 for 7 days.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room tenmperature, then washed with 5 M glycine. Cells were then lysed and sonicated in biorupter pico sonicator system.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3(Catalog NO. ND607, Vazyme).
The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: iTregs


title: 3543_OF1A_1-5-I1-H22


title: 3543_OF1A_1-5-I1-H21


title: Th1-likeiTregs replicate IP(H3R2me2s)

source_name: Th1-like iTregs

value: Th1-like iTregs


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026485LR01GC2-1-8-26]

description: Valproate, 500 mg/kg, Day 2, Repeat 1

source_name: Blood

value: whole blood

value: Valproate, 500 mg/kg, Day 2, Repeat 1


title: FDCs, WT, 1


title: LPH079_KH20-79885_02

city: Monrovia

first: Liangliang

last: Gao

address: 1225 S Shamrock Ave

institute: ChromoLogic

data_processing:
Isis (Analysis Software): 2.5.52.11
Bowtie (Aligner): 0.12.8
SAMtools: 0.1.19-isis-1.0.2
miRDeep*: 3.2
DESeq2: 1.0.17
Assembly: GRCh38
Supplementary files format and content: csv counts for all samples
Supplementary files format and content: csv counts

molecule: cytoplasmic RNA

source_name: Plasma

extract_protocol:
miRCL (ChromoLogic)
TruSeq

value: Plasma

value: Covid


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026484LR01GC1-3-8-26]

description: Valproate, 250 mg/kg, Day 2, Repeat 3

value: Valproate, 250 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_1-5-I1-H10

source_name: OF1A human BA46

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Th1 Input


title: LPH074_KH20-83769_01


title: iTregs Input


title: 3543_OF1A_1-5-I1-H9

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026483LR01GC1-2-8-26]

description: Valproate, 250 mg/kg, Day 2, Repeat 2

value: 8 wks

value: Valproate, 250 mg/kg, Day 2, Repeat 2


title: Th1 IP(H3R2me2s)


title: LPH074_KH20-83767_01


title: 3543_OF1A_1-5-I1-G9


title: LPH074_KH20-83738_01


title: 3543_OF1A_1-5-I1-G22


title: FDCs, WT, 3

value: WT


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026481LR01GB4-3-8-26]

description: Isoniazid, 3200 mg/kg, Day 2, Repeat 3

value: Isoniazid, 3200 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_1-5-I1-G21


title: 3543_OF1A_1-5-I1-G10


title: LPH074_KH20-83704_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026480LR01GB4-2-8-26]

description: Isoniazid, 3200 mg/kg, Day 2, Repeat 2

value: Isoniazid, 3200 mg/kg, Day 2, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026479LR01GB4-1-8-26]

description: Isoniazid, 3200 mg/kg, Day 2, Repeat 1

value: male

value: Isoniazid, 3200 mg/kg, Day 2, Repeat 1


title: Th1-likeiTregs Input


title: Th1-likeiTregs IP(H3R2me2s)


title: Kidney, -6A, High Salt 3

city: New Haven

first: Sravan

middle: Kumar

last: Perla

state: CT

address: 333 Cedar Street

department: Pharmacology

institute: Yale University

data_processing:
Partek Flow software (version 7.0, build 7.18.0130.2018 Partek Inc., St Louis, Missouri) and IPA
Paired-end reads were trimmed using a base quality score threshold of >24 and aligned to the Genome Reference Consortium Mouse Build 38 (mm10) with the STAR 2.5.3a aligner.
Quantification was carried out using the transcript model Ensembl Transcripts release 100.
Differential expression analysis was performed using the R package DESeq2 which provides a quantitative analysis using shrinkage estimators for dispersion and fold-change (Love et al., 2014).
Qlucore Omics Explorer 3.4 (Qlucore AB, Lund, Sweden) was used for data visualization, principal components analysis (PCA) and hierarchical clustering analysis (HCA) heatmap generation
Assembly: Genome Reference Consortium Mouse Build 38 (mm10) with the STAR 2.5.3a aligner.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include DESeq2 normalized values for each sample

source_name: Kidney

extract_protocol:
RNA was harvested from liver and kidney using Rneasy mini plus kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA Seq were prepared using SMARTER mRNA-Seq Library Prep Kit.

treatment_protocol: 12 week old adult male TG mice treated with and with out HSD.

value: Kidney

value: Hap -6A

value: High Salt


title: 3543_OF1A_1-5-I1-F22


title: LPH074_KH20-81356_01


title: 3543_OF1A_1-5-I1-F9


title: Kidney, -6A, High Salt 2


title: LPH074_KH20-81347_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026478LR01GB3-3-8-26]

city: Houston

first: yi

last: chai

address: pgpr

institute: Biostate AI

description: Isoniazid, 1600 mg/kg, Day 2, Repeat 3

data_processing:
Raw data from Illumina sequencer
illumina Adaptor Trim
HISAT2 Alignment
Assembly: NCBI GCF_015227675.2, Genome assembly mRatBN7.2
Supplementary files format and content: csv

extract_protocol:
Trizol based total RNA extraction method
RNA libraries for RNA-Seq were prepared by using mRNA capture based standard library preparation kit (Vazyme) following manufacturer's protocol.

value: whole blood

value: Isoniazid, 1600 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_1-5-I1-F21


title: LPH074_KH20-81340_01

value: Plasma

value: Covid


title: Th1-likeiTregs replicate Input

value: Th1-like iTregs


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026482LR01GC1-1-8-26]

description: Valproate, 250 mg/kg, Day 2, Repeat 1

value: Valproate, 250 mg/kg, Day 2, Repeat 1


title: Kidney, -6A, Basal 3

value: Normal Diet


title: 3543_OF1A_1-5-I1-F10

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026477LR01GB3-2-8-26]

description: Isoniazid, 1600 mg/kg, Day 2, Repeat 2

value: 8 wks

value: Isoniazid, 1600 mg/kg, Day 2, Repeat 2


title: LPH074_KH20-81273_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026476LR01GB3-1-8-26]

description: Isoniazid, 1600 mg/kg, Day 2, Repeat 1

value: male

value: Isoniazid, 1600 mg/kg, Day 2, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026475LR01GB2-3-8-26]

description: Isoniazid, 800 mg/kg, Day 2, Repeat 3

value: Isoniazid, 800 mg/kg, Day 2, Repeat 3


title: LPH074_KH20-79960_01


title: Kidney, -6A, Basal 2

value: Kidney

value: Hap -6A


title: Kidney, -6A, High Salt 1

value: High Salt


title: 3543_OF1A_1-5-I1-E9


title: Kidney, -6A, Basal 1


title: 3543_OF1A_1-5-I1-E22


title: LPH074_KH20-79955_01


title: LPH074_KH20-79947_01


title: 3543_OF1A_1-5-I1-E10


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026473LR01GB2-1-8-26]

description: Isoniazid, 800 mg/kg, Day 2, Repeat 1

value: whole blood

value: Isoniazid, 800 mg/kg, Day 2, Repeat 1


title: Liver, -6A, High Salt 4

value: Liver


title: Liver, -6A, High Salt 3


title: LPH074_KH20-79946_01

value: Plasma

value: Covid


title: 3543_OF1A_1-5-I1-D9


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026471LR01GB1-2-8-26]

description: Isoniazid, 400 mg/kg, Day 2, Repeat 2

value: Isoniazid, 400 mg/kg, Day 2, Repeat 2


title: Liver, -6A, High Salt 2


title: LPH074_KH20-79945_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026472LR01GB1-3-8-26]

description: Isoniazid, 400 mg/kg, Day 2, Repeat 3

value: Isoniazid, 400 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_1-5-I1-D22

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Liver, -6A, High Salt 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026470LR01GB1-1-8-26]

description: Isoniazid, 400 mg/kg, Day 2, Repeat 1

value: 8 wks

value: Isoniazid, 400 mg/kg, Day 2, Repeat 1


title: Liver, -6A, Basal 4

value: Normal Diet


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026469LR01GA4-3-8-26]

description: Carbon tetrachloride, 2 ml/kg, Day 2, Repeat 3

value: male


title: LPH074_KH20-79943_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026468LR01GA4-2-8-26]

description: Carbon tetrachloride, 2 ml/kg, Day 2, Repeat 2


title: 3543_OF1A_1-5-I1-D10

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-5-I1-E21


title: 3543_OF1A_1-5-I1-D21


title: Liver, -6A, Basal 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026467LR01GA4-1-8-26]

description: Carbon tetrachloride, 2 ml/kg, Day 2, Repeat 1


title: 3543_OF1A_1-5-I1-C22


title: Liver, -6A, Basal 2


title: 3543_OF1A_1-5-I1-C9


title: Liver, -6A, Basal 1


title: LPH074_KH20-79936_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026466LR01GA3-3-8-26]

description: Carbon tetrachloride, 1.5 ml/kg, Day 2, Repeat 3


title: Mouse Male MEF – Input

city: Los Angeles

first: Kathrin

last: Plath

institute: UCLA

description: Input DNA in Male MEFs

data_processing:
Trim: trim_galore (v0.4.1) with default parameters was used to trim DNA sequencing reads
Align: Bowtie2 (v2.2.9) with the default parameters was used to align reads
Filter: Samtools (v1.9) was used to remove reads with mapping quality less than 30, or marked by Picard MarkDuplicates (v2.1.0) as PCR duplicates
Count: Bedtools (v2.26.0) intersect was used to count reads in each genomic region (either 100kb windows every 25kb or 1Mb every 250kb)
Enrichment: read counts in each window were normalized by the total read counts in each sample. The ratio of the normalized reads in the pulldown to the input were used as inputs
Peaks: MACS2 (v2.2.7.1) using broad and max-gap=100 was used to call peaks
Assembly: mm9
Supplementary files format and content: bedgraph files represent normalized enrichment ratios in windows across the genome (either 100kb windows every 25kb or 1Mb every 250kb). Is_unmappable=yes mark unmappable genomic regions
Supplementary files format and content: peak files represent broad peaks called for XIST pulldown files samples compared to input
Library strategy: RAP-seq

source_name: Somatic

growth_protocol: Mouse embryonic stem cells (ESCs) were grown in mouse ESC medium containing knockout DMEM (Life Technologies), 15% FBS (Omega), 2mM L-glutamine (Life Technologies), 1x NEAA (Life Technologies), 0.1mM β-Mercaptoethanol (Sigma), 1x Penicillin/Streptomycin (Life Technologies) and 1000U/mL mouse LIF (homemade). To derive epiblast-like cells (EpiLCs), ESCs were first adjusted for at least 3 passages under feeder-free conditions on 0.5% gelatin-coated plates in the presence of 1000U/mL LIF and two inhibitors, CHIR99021 (3 μM) and PD0325901 (0.4 μM) (henceforth referred to as 2i+LIF) in serum-free N2B27 medium containing 1x N2 supplement and 1x B27 supplement (ThermoFisher), 2mM L-glutamine (Life Technologies), 1x NEAA (Life Technologies), 0.1mM β-Mercaptoethanol (Sigma) and 0.5 x Penicillin/Streptomycin (Life Technologies). Next, to induce EpiLC differentiation, cells were dissociated with accutase and seeded at a density of 20,000 cells/mL in N2B27 media supplemented with 20 ng/mL Activin A and 12 ng/mL bFGF on geltrex-coated plates. Fresh media was exchanged daily for both ESCs and EpiLCs. Mouse embryonic fibroblasts (MEFs) were cultured on non gelatin-coated plates under feeder-free conditions in DMEM (Life Technologies), 15% FBS (Omega), 2mM L-glutamine (Life Technologies), 1x NEAA (Life Technologies), 0.1mM β-Mercaptoethanol (Sigma) and 1x Penicillin/Streptomycin (Life Technologies). Fresh media was exchanged once every 3 days.

extract_protocol:
5× 106cells were harvested per condition after accutase-mediated dissociation and RAP-seq was performed, based on the protocol adapted from Engreitz et al. (Engreitz et al., 2013). Briefly, cells were incubated for 45min with freshly made 2mM DSG in PBS at room temperature, crosslinked with 3% formaldehyde for 10min and quenched with 500mM glycine. Cells were subsequently pelleted at 1,500xg for 5min at 4˚C, aliquoted into vials of 10 million cells each, and subjected to lysate preparation as follows: Cell pellets were resuspended in 10ml of nuclear extraction buffer LB1 containing50mM HEPES-KOH (pH 7.5), 140mM NaCl, 1mM EDTA, 10% (vol/vol) glycerol, 0.5% (vol/vol) NP-40/Igepal CA-630 and 0.25% (vol/vol) Triton X-100, and incubated for 10min with rotation at 4°C, then pelleted at 2000xg for 5min and the same procedure was performed with buffer LB2, which contains 10mM Tris-HCL (pH 8.0), 200mM NaCl, 1mM EDTA and 0.5mM EGTA. For cell lysis, nuclei were resuspended in 300μL of buffer LB3 containing 10mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% (wt/vol) sodium deoxycholate and 0.5% (vol/vol) N-lauroylsarcosine, then sonicated on ice using the Misonix S-400 sonicator with microtip (model number: U1240A0418) for 2min at an amplitude of 12 with 1sec pulses intermitted by 3sec pauses. Next, chromatin was further digested using TURBO DNase at a concentration of 0.1-0.4U/μl at 37°C for 15min. The digestion was stopped by the addition of DNase Stop Solution (mixture of EDTA and EGTA). 5% of each sample was set aside as the input control, while the remaining sample was used for the actual pulldown. The RNA pulldown was performed using 50pmol of 90nt-long biotinylated oligonucleotide probes for every 5× 106cells and Streptavidin C1 beads. DNA was eluted by RNase H digestion, and the crosslinks were reversed by proteinase K digestion of the eluted DNA at 60°C.
DNA libraries were prepared using NEB Next Ultra End Repair/dA-Tailing Module (NEB) and TruSeq DNA adapters (Illumina) were ligated using Quick Ligase (NEB). Libraries were amplified by KAPA HiFi Polymerase, pooled and sequenced on the Illumina HiSeq 6000 platform to generate 50bp pair-end reads.

treatment_protocol: In addition to growing each cell type in its appropriate media condition as described under "growth protocol", cells were not treated with any additional agent(s).

value: Somatic

tag: library strategy

value: RAP-Seq

tag: experiment type

value: Input


title: 3543_OF1A_1-5-I1-C21

city: La Jolla

first: Joseph

last: Ecker

institute: HHMI-Salk-Institute

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn


title: LPH074_KH20-79935_01


title: LPH074_KH20-79944_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026465LR01GA3-2-8-26]

description: Carbon tetrachloride, 1.5 ml/kg, Day 2, Repeat 2

value: whole blood


title: 3543_OF1A_1-5-I1-C10


title: LPH074_KH20-79934_01


title: 3543_OF1A_1-5-I1-B9


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026474LR01GB2-2-8-26]

description: Isoniazid, 800 mg/kg, Day 2, Repeat 2

value: Isoniazid, 800 mg/kg, Day 2, Repeat 2


title: Mouse Male MEF – XIST Pulldown

description: RAP-Seq using probes targeting Xist in Male MEFs

value: XIST RAP


title: Mouse Female MEF – Input

description: Input DNA in Female MEFs


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [R23026464LR01GA3-1-8-26]

description: Carbon tetrachloride, 1.5 ml/kg, Day 2, Repeat 1


title: LPH074_KH20-79931_01

value: Plasma


title: LPH074_KH20-79939_01

value: Covid


title: LPH074_KH20-79938_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026463LR01-GA2-3-8-26]

description: Carbon tetrachloride, 1 ml/kg, Day 2, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026462LR01-GA2-2-8-26]

description: Carbon tetrachloride, 1 ml/kg, Day 2, Repeat 2


title: 3543_OF1A_1-5-I1-B21


title: LPH074_KH20-79928_01


title: LPH074_KH20-79927_01


title: Mouse Female MEF – XIST Pulldown

description: RAP-Seq using probes targeting Xist in Female MEFs


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026461LR01-GA2-1-8-26]

description: Carbon tetrachloride, 1 ml/kg, Day 2, Repeat 1


title: Mouse Female EpiLC R3 – Input

description: Input DNA in EpiLCs (Rep3)

source_name: ESC (EpiLC)

value: ESC (EpiLC)


title: LPH074_KH20-79926_01


title: 3543_OF1A_1-5-I1-B10


title: 3543_OF1A_1-5-I1-B22


title: Mouse Female Day 4 EpiLC R2 – XIST Pulldown

description: RAP-Seq using probes targeting Xist in D4 EpiLCs (Rep2)


title: LPH074_KH20-79913_01


title: 3543_OF1A_1-5-I1-A9


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026460LR01-GA1-3-8-26]

description: Carbon tetrachloride, 0.5 ml/kg, Day 2, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026459LR01-GA1-2-8-26]

description: Carbon tetrachloride, 0.5 ml/kg, Day 2, Repeat 2


title: Mouse Female Day 2 EpiLC R2 – XIST Pulldown

description: RAP-Seq using probes targeting Xist in D2 EpiLCs (Rep2)


title: 3543_OF1A_1-5-I1-A21


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026458LR01-GA1-1-8-26]

description: Carbon tetrachloride, 0.5 ml/kg, Day 2, Repeat 1


title: LPH074_KH20-79912_01


title: LPH074_KH20-79904_01


title: LPH074_KH20-79903_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026457LR01-1-3-8-26]

description: Sodium chloride, 0.9%, Day 2, Repeat 3

value: Sodium chloride, 0.9%, Day 2, Repeat 3


title: Mouse Female EpiLC R1 – Input

description: Input DNA in EpiLCs (Rep1) (re-analysis of GSM4929715)


title: 3543_OF1A_1-5-I1-A10

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Mouse Female Day 4 EpiLC R1 – XIST Pulldown

description: RAP-Seq using probes targeting Xist in D4 EpiLCs (Rep1) (re-analysis of GSM4929714)


title: 3543_OF1A_1-4-I1-P8

value: Female


title: LPH074_KH20-79896_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026456LR01-1-2-8-26]

description: Sodium chloride, 0.9%, Day 2, Repeat 2

value: 8 wks

value: Sodium chloride, 0.9%, Day 2, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026455LR01-1-1-8-26]

description: Sodium chloride, 0.9%, Day 2, Repeat 1

value: Sodium chloride, 0.9%, Day 2, Repeat 1


title: Mouse Female Day 2 EpiLC R1 – XIST Pulldown

description: RAP-Seq using probes targeting Xist in D2 EpiLCs (Rep1) (re-analysis of GSM4929713)


title: LPH074_KH20-79892_01


title: 3543_OF1A_1-4-I1-P7


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026453LR01-GC4-2-8-25]

description: Valproate, 2000 mg/kg, Day 1, Repeat 2

value: male

value: Valproate, 2000 mg/kg, Day 1, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026454LR01-GC4-3-8-25]

description: Valproate, 2000 mg/kg, Day 1, Repeat 3

value: Valproate, 2000 mg/kg, Day 1, Repeat 3


title: 3543_OF1A_1-4-I1-P20

value: nuclear RNA + genomic DNA


title: Wild type, male, perigonadal white adipose tissue, replicate 3

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

data_processing:
The sequenced reads (raw reads) often contain low quality reads and adapters, which will affect the analysis quality. So it's necessary to filter the raw reads and get the clean reads. The filtering process is as follows: 1. Remove reads containing adapters. 2.  Remove reads containing N > 10% (N represents the base cannot be determined). 3. Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base. Sequences of adaptors: 5' Adapter:   5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'; 3' Adapter(The underlined 6bp bases is Index):  5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG-3'
Mapping with STAR version 2.7.3a
Gene-level read counts were obtained with summarizeOverlaps, mode = ’Union’, package GenomicAlignments v1.30.0
Normalization with DESeq2 (version 1.28.1)
Assembly: GRCm38.101
Supplementary files format and content: tab-delimited file with normalized counts

source_name: perigonadal white adipose tissue

growth_protocol: Animals were maintained in ICV cages with water and standard mouse chow according to the directive 2010/63/EU, German national laws and GMC housing conditions (www.mouseclinic.de).

extract_protocol:
Total RNA (including miRNA and other small RNA molecules) was extracted with the RNeasy Mini kit (Qiagen) including Trizol treatment.
Directional mRNA library done by Novogene. mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: no

value: perigonadal white adipose tissue


title: Wild type, male, perigonadal white adipose tissue, replicate 2


title: Mouse Female EpiLC R2 – Input

description: Input DNA in EpiLCs (Rep2)

value: RAP-Seq

value: Input


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026452LR01-GC4-1-8-25]

description: Valproate, 2000 mg/kg, Day 1, Repeat 1

value: whole blood

value: Valproate, 2000 mg/kg, Day 1, Repeat 1


title: Wild type, male, perigonadal white adipose tissue, replicate 1


title: LPH074_KH20-79884_01

value: Plasma

value: Covid


title: 3543_OF1A_1-5-I1-A22

address: 10010 North Torrey Pines Road


title: 3543_OF1A_1-4-I1-O7


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026451LR01-GC3-3-8-25]

description: Valproate, 1000 mg/kg, Day 1, Repeat 3

value: Valproate, 1000 mg/kg, Day 1, Repeat 3


title: 3543_OF1A_1-4-I1-O20

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: LPH070_KH20-74379_01


title: Wild type, female, perigonadal white adipose tissue, replicate 4

value: female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026450LR01-GC3-2-8-25]

description: Valproate, 1000 mg/kg, Day 1, Repeat 2

value: 8 wks

value: Valproate, 1000 mg/kg, Day 1, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026449LR01-GC3-1-8-25]

description: Valproate, 1000 mg/kg, Day 1, Repeat 1

value: Valproate, 1000 mg/kg, Day 1, Repeat 1


title: 3543_OF1A_1-4-I1-O19

value: Female


title: LPH070_KH20-74377_01


title: LPH074_KH20-79890_01


title: Wild type, female, perigonadal white adipose tissue, replicate 3


title: Wild type, female, perigonadal white adipose tissue, replicate 2


title: LPH070_KH20-70160_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026448LR01-GC2-3-8-25]

description: Valproate, 500 mg/kg, Day 1, Repeat 3

value: male

value: Valproate, 500 mg/kg, Day 1, Repeat 3


title: 3543_OF1A_1-4-I1-P19

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-4-I1-N8


title: LPH070_KH20-64853_01


title: Wild type, female, perigonadal white adipose tissue, replicate 1

value: perigonadal white adipose tissue


title: 3543_OF1A_1-4-I1-N20


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026447LR01-GC2-2-8-25]

description: Valproate, 500 mg/kg, Day 1, Repeat 2

value: Valproate, 500 mg/kg, Day 1, Repeat 2


title: LPH070_KH20-74381_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026446LR01-GC2-1-8-25]

description: Valproate, 500 mg/kg, Day 1, Repeat 1

value: Valproate, 500 mg/kg, Day 1, Repeat 1


title: LPH070_KH20-48030_01


title: 3543_OF1A_1-4-I1-N19


title: 3543_OF1A_1-4-I1-O8


title: Wild type, female, perigonadal white adipose tissue, replicate 5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026445LR01-GC1-3-8-25]

description: Valproate, 250 mg/kg, Day 1, Repeat 3

value: whole blood

value: Valproate, 250 mg/kg, Day 1, Repeat 3


title: LPH070_KH20-65147_01

value: Plasma


title: 3543_OF1A_1-4-I1-M7


title: U90926 ko, male, perigonadal white adipose tissue, replicate 3


title: LPH070_KH20-34756_01

value: Covid


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026443LR01-GC1-1-8-25]

description: Valproate, 250 mg/kg, Day 1, Repeat 1

value: Valproate, 250 mg/kg, Day 1, Repeat 1


title: LPH070_KH20-34516_01


title: 3543_OF1A_1-4-I1-M8

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026442LR01-GB4-3-8-25]

description: Isoniazid, 3200 mg/kg, Day 1, Repeat 3

value: Isoniazid, 3200 mg/kg, Day 1, Repeat 3


title: U90926 ko, male, perigonadal white adipose tissue, replicate 4


title: LPH070_KH20-32336_01


title: 3543_OF1A_1-4-I1-N7


title: U90926 ko, female, perigonadal white adipose tissue, replicate 4

value: female


title: 3543_OF1A_1-4-I1-M20


title: LPH070_KH20-27493_01


title: U90926 ko, female, perigonadal white adipose tissue, replicate 5


title: 3543_OF1A_1-4-I1-M19


title: U90926 ko, male, perigonadal white adipose tissue, replicate 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026444LR01-GC1-2-8-25]

description: Valproate, 250 mg/kg, Day 1, Repeat 2

value: 8 wks

value: Valproate, 250 mg/kg, Day 1, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026441LR01-GB4-2-8-25]

description: Isoniazid, 3200 mg/kg, Day 1, Repeat 2

value: Isoniazid, 3200 mg/kg, Day 1, Repeat 2


title: LPH070_KH20-23513_01


title: U90926 ko, female, perigonadal white adipose tissue, replicate 3


title: U90926 ko, female, perigonadal white adipose tissue, replicate 2


title: U90926 ko, male, perigonadal white adipose tissue, replicate 2

value: male


title: 3543_OF1A_1-4-I1-L8

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026440LR01-GB4-1-8-25]

description: Isoniazid, 3200 mg/kg, Day 1, Repeat 1

value: Isoniazid, 3200 mg/kg, Day 1, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026439LR01-GB3-3-8-25]

description: Isoniazid, 1600 mg/kg, Day 1, Repeat 3

value: Isoniazid, 1600 mg/kg, Day 1, Repeat 3


title: LPH070_KH20-17801_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026438LR01-GB3-2-8-25]

description: Isoniazid, 1600 mg/kg, Day 1, Repeat 2

value: Isoniazid, 1600 mg/kg, Day 1, Repeat 2


title: 3543_OF1A_1-4-I1-L20

value: nuclear RNA + genomic DNA


title: LPH070_KH20-17787_01


title: U90926 ko, female, perigonadal white adipose tissue, replicate 1

value: perigonadal white adipose tissue


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026437LR01-GB3-1-8-25]

description: Isoniazid, 1600 mg/kg, Day 1, Repeat 1

value: whole blood

value: Isoniazid, 1600 mg/kg, Day 1, Repeat 1


title: Wild-type MaleMouse22 [multiome]

first: Michel

middle: A

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

library_source: other

data_processing:
library strategy: Multiome (both RNAseq and ATACseq)
Single-nuclei Multiome data (ATAC  + Gene Expression) were processed using the Cell Ranger ARC pipeline version 2.0.0 with default parameters.
Samples were aligned to the CellRanger mm10 reference genome (specifically, refdata-cellranger-arc-mm10-2020-A-2.0.0).  Introns were included in the gene expression counts.
Assembly: mm10
Supplementary files format and content: Count matrices for cell barcodes in Hierarchical Data Format HDF5.  File includes both the Gene Expression UMI count matrix and the ATAC peaks fragment count matrix.
Supplementary files format and content: BED-like tabular file listing all unique fragments captured by the ATAC assay in tab-separated values (TSV) format.
Supplementary files format and content: BED-like tabular file listing all ATAC peaks called by the pipeline and their nearest gene annotation.  TSV format.
Supplementary files format and content: Metadata file that contains Gene Expression and ATAC QC metrics for every barcode in comma-separated values (CSV) format.

molecule: other

source_name: Pituitary gland

growth_protocol: The frozen murine pituitary used for multiome was obtained collected from a wild-type (wt) male C57Bl6 mouse, and kept at -80C until processing.

extract_protocol:
Briefly, and all on ice, RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCl2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. The pituitary was homogenized in a dounce glass homogenizer (1ml, VWR cat# 71000-514), and the homogenate filtered through a 40 mm cell strainer. An equal volume of 50% OptiPrep was added, and the gradient centrifuged (SW41 rotor at 9200rpm; 4C; 25min). Nuclei were collected from the interphase, washed, resuspended in 1X nuclei buffer for sn multiome (10X Genomics).
sn Multiome was performed as described (10x Genomics, Pleasanton, CA; (24)), following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guidelines. Nuclei were filtered and counted on a Countess instrument. The amount of nuclei loaded on the chip was determined based on the 10X Genomics protocol. The 10X chip (Chromium Single Cell 3’ Chip kit J  PN-200264) was loaded to target 10,000 nuclei final. After transposition, linear amplification was performed in the emulsion and cDNA was amplified before the RNA and ATAC library constructions were performed following the Chromium multiome protocol. The library was tagged with an index for multiplexing (Chromium i7 Sample Index Plate N Set A for ATAC PN-3000427; Chromium i7 Sample Dual Index Plate TT Set A for ATAC PN-3000431). Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the NYGC on Illumina Novaseq using paired-end reads.

treatment_protocol: The frozen pituitary was homogenized in a glass homegenizer as described in Mendelev Star Protocol 2022.

value: 10 weeks

value: frozen pituitary

tag: molecule type

value: nuclear mRNA & DNA

value: Male


title: 3543_OF1A_1-4-I1-K8

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age


title: 3543_OF1A_1-4-I1-K7

tag: Sex


title: LPH070_KH20-17784_01

tag: tissue

value: Plasma

value: Covid


title: KO1_ISC

city: Guangzhou

first: Ye-Guang

last: Chen

address: 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Quality control was performed using FastQC v0.19.7.
For bulk RNA-seq, sequencing reads were aligned to mm10 mouse genome reference (GRCh38) using STAR with default parameter (Dobin et al., 2013).
For small RNA-seq, clean data was mapped to mm10 mouse genome reference (GRCh38) and miRbase with Bowtie2 and the counts were summarized and normalized by RDeseq2.
Assembly: Sequencing reads were aligned using GRCm38/mm10 assembly of the mouse genome.
Supplementary files format and content: gene_count_matrix.csv: Comma-delimited text file includes reads counts for each sample.

source_name: Intestinal epithelial cells

extract_protocol:
Total RNA was extracted and purified by using TRIZOL reagent (Thermo Fisher Scientific). 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA integrity was measured using electrophoresis. Subsequently, First-strand cDNA was generated using random hexamer primers. Then, a second-strand cDNA was synthesized. A-Tailing Mix and RNA Index Adapters followed to subjected to the end of the cDNA. The cDNA fragments were amplified by PCR and the product was qualified by Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and the 2100 Bioanalyzer (Agilent). After it, the products were denatured and circularized to collect the final library.
Bulk RNA-seq and small RNA-seq

value: Intestinal epithelial cells

value: Dgcr8 KO_1

tag: treatment


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026434LR01-GB2-1-8-25]

description: Isoniazid, 800 mg/kg, Day 1, Repeat 1

value: 8 wks

value: male

value: Isoniazid, 800 mg/kg, Day 1, Repeat 1


title: KO_miRNA

source_name: Intestinal epithelium

value: Intestinal epithelium

tag: cell line

value: Dgcr8 KO


title: WT_miRNA

value: WT

value: Ethanol


title: 3543_OF1A_1-4-I1-K19

tag: brain region

value: Female

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026435LR01-GB2-2-8-25]

description: Isoniazid, 800 mg/kg, Day 1, Repeat 2

value: whole blood

value: Isoniazid, 800 mg/kg, Day 1, Repeat 2


title: LPH070_KH20-16367_01


title: 3543_OF1A_1-4-I1-K20

tag: molecule subtype


title: LPH070_KH20-16281_01


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026432LR01-GB1-2-8-25]

description: Isoniazid, 400 mg/kg, Day 1, Repeat 2

value: Isoniazid, 400 mg/kg, Day 1, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026436LR01-GB2-3-8-25]

description: Isoniazid, 800 mg/kg, Day 1, Repeat 3

value: Isoniazid, 800 mg/kg, Day 1, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026433LR01-GB1-3-8-25]

description: Isoniazid, 400 mg/kg, Day 1, Repeat 3

value: Isoniazid, 400 mg/kg, Day 1, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026431LR01-GB1-1-8-25]

description: Isoniazid, 400 mg/kg, Day 1, Repeat 1

value: Isoniazid, 400 mg/kg, Day 1, Repeat 1


title: KH20-34053

value: Plasma

value: Covid


title: 3543_OF1A_1-4-I1-J20

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: KH20-34730


title: WT2_ISC

value: Intestinal epithelial cells

tag: cell type


title: LPH070_KH20-17803_01


title: KH20-34740


title: WT1_ISC

tag: genotype


title: KH20-23566


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026429LR01-GA4-2-8-25]

description: Carbon tetrachloride, 2 ml/kg, Day 1, Repeat 2

value: 8 wks

value: male


title: KH20-34024


title: KO1_Org

value: Dgcr8 KO_1


title: 3543_OF1A_1-4-I1-I7


title: 3543_OF1A_1-4-I1-I20


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026430LR01-GA4-3-8-25]

description: Carbon tetrachloride, 2 ml/kg, Day 1, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026426LR01-GA3-2-8-25]

description: Carbon tetrachloride, 1.5 ml/kg, Day 1, Repeat 2


title: KO1_5FU_Crypts

value: Intestinal epithelium


title: 3543_OF1A_1-4-I1-I8


title: KH20-48033


title: 3543_OF1A_1-4-I1-J8


title: WT2_Org

value: Ethanol