title: Drought6_71d_rewater1_rep2


title: soleus, Male, TH, Chow, Age 20 Week, Replicate 6

status: Public on Nov 30 2023

type: SRA

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

country: USA

institute: Marshall University School of Medicine

library_source: transcriptomic

data_processing:
Reads were trimmed using Trimmomatic version 0.39 in PE mode, to remove Illumina adapters, to remove the first 12 bases from the reads, to crop to a maximum of 37 bases in length, to remove low quality reads, and to filter any reads less than 25 bases in length. Parameters: ILLUMINACLIP TruSeq3-PE-2.fa:2:30:10 HEADCROP:12 CROP:37 SLIDINGWINDOW:4:15 MINLEN:25
Reads were aligned to the mouse genomeGRCm39 using HISAT2 version 2.2.1 with default parameters
Alignment files were sorted by name using samtools sort -n with samtools version
Mate coordinate and insert size fields were added to alignment files with samtools fixmate using samtools version
Alignment files were sorted by position using samtools sort with samtools version
Duplicate reads were removed using samtools markdup -r with samtools version
Gene level counts were generated using the makeTxDbFromGFF and exonsBy functions from the Bioconductor package GenomicFeatures, version and the summarizeOverlaps function from the Bioconductor package GenomicAlignments, version. The latter was run with parameters mode="IntersectionStrict", singleEnd=F, ignore.strand=T, fragments=F
Gene counts were normalized using the DESeq function, and FPKM values computed using the fpkm function from Bioconductor package DESeq2 version
Assembly: Genome GRCm39 Mus_musculus.GRCm39.dna.toplevel.fa from Ensembl. Gene annotations used in creating read counts are Ensembl Genes version 108, Mus_musculus.GRCm39.108.gtf
Supplementary files format and content: raw_counts.csv is a comma deliminted file containing the raw read counts from each sample
Supplementary files format and content: normalized_counts.csv is a comma delimited file containing the normalized counts (using the DESeq function from Bioconductor package DESeq2) from each sample
Supplementary files format and content: fpkm.csv is a comma delimited file containing the FPKM values (computed using the fpkm function from Bioconductor package DESeq2) for each sample

molecule: total RNA

organism: Mus musculus

source_name: soleus

extract_protocol:
Total RNA was isolated from the tissue using RNeasy Plus Universal Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
All RNA samples were assessed using the Bioanalyzer 2100 and quantified using the Thermo Fisher Qubit RNA assay. Each RNA sample with a RIN value above 8 and a quantity of 1000ng was utilized to generate a Poly(A)-based RNAseq library following the Illumina TruSeq stranded mRNA protocol. Briefly, the poly(A) RNAs were purified using oligo dT magnetic beads and were then fragmented with divalent cations, followed by reverse transcription into cDNA. The Illumina paired-end oligo adapters were ligated to the cDNA fragments, and the RNAseq libraries were amplified using PCR. The finished libraries were purified and analyzed on an Agilent Bioanalyzer 2100, revealing an average library size ranging from 285 to 300 base pairs. To determine the quantity of these libraries, they were further measured using the Thermo Fisher Qubit HS dsDNA assay.

treatment_protocol: At 4 weeks of age, male and female TALLYHO/Jng (TH) and C57BL/6J (B6) mice were weaned onto either standard chow or high fat diets and maintained on the respective diets. After 1 and 16 weeks of feeding (5 and 20 weeks of age), mice were euthanized by CO2 inhalation followed by cervical dislocation and exsanguination via cardiac puncture. Tissues including liver, gonadal fat, soleus muscle, and pancreas were then collected for RNA isolation.

tag: tissue

value: soleus

tag: Sex

value: M

tag: strain

value: TH

tag: diet

value: Chow

tag: age


title: fat, Male, TH, Chow, Age 20 Week, Replicate 5

source_name: fat

value: fat


title: Drought5_71d_rewater1_rep2

city: Tsukuba

first: FUMIYUKI

last: SOMA

state: Ibaraki

address: 2-1-2 Kan-non-dai

department: Institute of Crop Science

country: Japan

institute: National Agriculture and Food Research Organization

data_processing:
Reads were mapped to the IRGSP-1.0 genome assembly and MSU7 gene models using the STAR aligner (Dobin et al., 2013)
Read counts were quantified using the featureCounts (Liao et al., 2014) with option” -S 2 -p -B -C -T”.
Supplementary files format and content: Tab-delimited text files include row counts for each Sample

organism: Oryza sativa

growth_protocol: Rice plants were grown in a growth chamber under a 14 h light/10 h dark photoperiod, with 50% R.H. at daytime and 60% R.H. at nighttime. The temperature in the growth chamber varied from 25°C to 30℃ at daytime,

extract_protocol:
Total RNA was extracted using TRIzol RNA Isolation Reagents (Thermo Fisher) according to manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional mRNA-seq kit (New England Biolabs)

treatment_protocol: The water level in each pot was maintained at 6 cm above the bottom of the pot under WW conditions. Drought stress was initiated at each indicated days after sowing by withdrawing water supply.

tag: genotype

value: Nipponbare

tag: treatment


title: Pancreas, Male, TH, Chow, Age 20 Week, Replicate 3

source_name: Pancreas

value: Pancreas


title: Pancreas, Male, TH, Chow, Age 20 Week, Replicate 2


title: soleus, Male, TH, Chow, Age 20 Week, Replicate 4


title: liver, Male, TH, Chow, Age 20 Week, Replicate 4

source_name: liver

value: liver


title: Drought6_71d_rewater1_rep1


title: Drought5_71d_rewater1_rep3


title: liver, Male, TH, Chow, Age 20 Week, Replicate 3


title: Drought5_71d_rewater1_rep1


title: soleus, Male, TH, Chow, Age 20 Week, Replicate 3


title: Well-watered3_71d_rewater1_rep1


title: Well-watered3_71d_rewater1_rep3


title: Well-watered3_71d_rewater1_rep2


title: Well-watered3_80d_rep1


title: fat, Male, TH, Chow, Age 20 Week, Replicate 4


title: soleus, Male, TH, Chow, Age 20 Week, Replicate 1


title: liver, Male, TH, Chow, Age 20 Week, Replicate 2


title: Well-watered3_74d_rep1


title: Drought6_71d_rep2


title: fat, Male, TH, Chow, Age 20 Week, Replicate 3


title: liver, Male, TH, Chow, Age 20 Week, Replicate 1


title: fat, Male, TH, Chow, Age 20 Week, Replicate 1


title: Pancreas, Male, B6, HF, Age 5 Week, Replicate 6

value: HF


title: fat, Male, B6, HF, Age 5 Week, Replicate 6


title: soleus, Male, B6, HF, Age 5 Week, Replicate 7


title: Well-watered3_71d_rep3


title: Drought5_71d_rep1


title: Well-watered3_71d_rep2


title: Well-watered3_71d_rep1


title: Drought4_86d_rep3


title: soleus, Male, TH, Chow, Age 20 Week, Replicate 2


title: Pancreas, Male, B6, HF, Age 5 Week, Replicate 5


title: Drought4_86d_rep2


title: Drought6_71d_rep3


title: Pancreas, Male, B6, HF, Age 5 Week, Replicate 3


title: Drought4_86d_rep1


title: Pancreas, Male, B6, HF, Age 5 Week, Replicate 2


title: Drought6_71d_rep1


title: soleus, Male, B6, HF, Age 5 Week, Replicate 6


title: Drought3_86d_rep2


title: Pancreas, Male, B6, HF, Age 5 Week, Replicate 1


title: Drought3_86d_rep3


title: Drought3_86d_rep1


title: Drought5_71d_rep3


title: Drought5_71d_rep2


title: fat, Male, TH, Chow, Age 20 Week, Replicate 2


title: Well-watered2_86d_rep3


title: fat, Male, B6, HF, Age 5 Week, Replicate 5


title: Well-watered2_86d_rep2


title: liver, Male, B6, HF, Age 5 Week, Replicate 5


title: Drought6_74d_rep1


title: Drought2_86d_rep3


title: Pancreas, Male, B6, HF, Age 5 Week, Replicate 4


title: Drought2_86d_rep1


title: Drought2_86d_rep2


title: soleus, Male, B6, HF, Age 5 Week, Replicate 4


title: Drought1_86d_rep3


title: Well-watered2_86d_rep1


title: fat, Male, B6, HF, Age 5 Week, Replicate 3


title: liver, Male, B6, HF, Age 5 Week, Replicate 4


title: soleus, Male, B6, HF, Age 5 Week, Replicate 3


title: liver, Male, B6, HF, Age 5 Week, Replicate 6


title: soleus, Male, B6, HF, Age 5 Week, Replicate 2


title: soleus, Male, B6, HF, Age 5 Week, Replicate 1


title: liver, Male, B6, HF, Age 5 Week, Replicate 2


title: Drought6_68d_rep3


title: Well-watered1_86d_rep3


title: Well-watered1_86d_rep2


title: Drought6_68d_rep2


title: Well-watered1_86d_rep1


title: Drought1_86d_rep1


title: Drought1_86d_rep2


title: soleus, Male, B6, HF, Age 5 Week, Replicate 5


title: fat, Male, B6, HF, Age 5 Week, Replicate 2


title: liver, Male, B6, HF, Age 5 Week, Replicate 1


title: fat, Male, B6, HF, Age 5 Week, Replicate 4


title: Drought6_68d_rep1


title: fat, Male, B6, HF, Age 5 Week, Replicate 1


title: Drought5_68d_rep2


title: liver, Male, B6, HF, Age 20 Week, Replicate 6


title: fat, Male, B6, HF, Age 20 Week, Replicate 6


title: soleus, Male, B6, HF, Age 20 Week, Replicate 6


title: Well-watered3_68d_rep3


title: Drought5_68d_rep3


title: fat, Male, B6, HF, Age 20 Week, Replicate 5


title: soleus, Male, B6, HF, Age 20 Week, Replicate 5


title: Drought5_68d_rep1


title: soleus, Male, B6, HF, Age 20 Week, Replicate 4


title: Drought6_65d_rep3


title: Well-watered3_68d_rep1


title: Well-watered3_68d_rep2


title: fat, Male, B6, HF, Age 20 Week, Replicate 4


title: liver, Male, B6, HF, Age 20 Week, Replicate 5


title: Drought5_65d_rep3


title: Drought6_65d_rep2


title: Drought5_65d_rep1


title: liver, Male, B6, HF, Age 20 Week, Replicate 4


title: Drought6_65d_rep1


title: soleus, Male, B6, HF, Age 20 Week, Replicate 3


title: Well-watered3_65d_rep3


title: fat, Male, B6, HF, Age 20 Week, Replicate 3


title: liver, Male, B6, HF, Age 20 Week, Replicate 3


title: soleus, Male, B6, HF, Age 20 Week, Replicate 2


title: Drought5_65d_rep2


title: Well-watered3_65d_rep2


title: Drought4_80d_rep3


title: Drought4_80d_rep2


title: soleus, Male, B6, HF, Age 20 Week, Replicate 1


title: fat, Male, B6, HF, Age 20 Week, Replicate 1


title: liver, Male, B6, HF, Age 20 Week, Replicate 2


title: liver, Male, B6, HF, Age 20 Week, Replicate 1


title: Drought4_80d_rep1


title: fat, Male, B6, HF, Age 20 Week, Replicate 2


title: Pancreas, Male, B6, HF, Age 20 Week, Replicate 6


title: Pancreas, Male, B6, HF, Age 20 Week, Replicate 7


title: Drought3_80d_rep3


title: Drought3_80d_rep2


title: Pancreas, Male, B6, HF, Age 20 Week, Replicate 5


title: Drought3_80d_rep1


title: liver, Male, B6, HF, Age 5 Week, Replicate 3


title: Well-watered2_80d_rep3


title: Pancreas, Male, B6, HF, Age 20 Week, Replicate 4


title: Well-watered3_65d_rep1


title: Drought2_80d_rep3


title: Drought2_80d_rep2


title: Pancreas, Male, B6, HF, Age 20 Week, Replicate 1


title: Pancreas, Male, B6, Chow, Age 5 Week, Replicate 6


title: Well-watered2_80d_rep2


title: Pancreas, Male, B6, Chow, Age 5 Week, Replicate 5


title: Pancreas, Male, B6, HF, Age 20 Week, Replicate 2


title: Pancreas, Male, B6, Chow, Age 5 Week, Replicate 4


title: Drought2_80d_rep1


title: Pancreas, Male, B6, Chow, Age 5 Week, Replicate 3


title: Drought1_80d_rep2


title: Pancreas, Male, B6, Chow, Age 5 Week, Replicate 2


title: Well-watered2_80d_rep1


title: Pancreas, Male, B6, HF, Age 20 Week, Replicate 3


title: liver, Male, B6, Chow, Age 5 Week, Replicate 6


title: Pancreas, Male, B6, Chow, Age 5 Week, Replicate 1


title: soleus, Male, B6, Chow, Age 5 Week, Replicate 6


title: Well-watered1_80d_rep3


title: Drought1_80d_rep1


title: Well-watered1_80d_rep1


title: Drought6_62d_rep2


title: fat, Male, B6, Chow, Age 5 Week, Replicate 6


title: soleus, Male, B6, Chow, Age 5 Week, Replicate 5


title: liver, Male, B6, Chow, Age 5 Week, Replicate 5


title: Drought5_62d_rep3


title: Drought1_80d_rep3


title: fat, Male, B6, Chow, Age 5 Week, Replicate 5


title: liver, Male, B6, Chow, Age 5 Week, Replicate 4


title: Drought5_62d_rep2


title: fat, Male, B6, Chow, Age 5 Week, Replicate 4


title: Well-watered3_62d_rep3


title: soleus, Male, B6, Chow, Age 5 Week, Replicate 4


title: Well-watered3_62d_rep2


title: Well-watered1_80d_rep2


title: Drought5_62d_rep1


title: fat, Male, B6, Chow, Age 5 Week, Replicate 3


title: Well-watered3_62d_rep1


title: liver, Male, B6, Chow, Age 5 Week, Replicate 3


title: Drought6_59d_rewater1_rep3


title: Drought6_62d_rep3


title: soleus, Male, B6, Chow, Age 5 Week, Replicate 3


title: Drought6_59d_rewater1_rep1


title: liver, Male, B6, Chow, Age 5 Week, Replicate 2


title: Drought6_59d_rewater1_rep2


title: Drought5_59d_rewater1_rep3


title: fat, Male, B6, Chow, Age 5 Week, Replicate 2


title: soleus, Male, B6, Chow, Age 5 Week, Replicate 2


title: Drought5_59d_rewater1_rep2


title: liver, Male, B6, Chow, Age 5 Week, Replicate 1


title: fat, Male, B6, Chow, Age 5 Week, Replicate 1


title: Drought5_59d_rewater1_rep1


title: Well-watered3_59d_rewater1_rep3


title: soleus, Male, B6, Chow, Age 20 Week, Replicate 6


title: Drought6_62d_rep1


title: soleus, Male, B6, Chow, Age 5 Week, Replicate 1


title: liver, Male, B6, Chow, Age 20 Week, Replicate 6


title: GCs_CON_1

city: Changchun

first: kening

last: liu

state: jilin

address: Xian road

country: China

institute: jilin university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

organism: Sus scrofa

source_name: follicle granulosa cells

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: follicle granulosa cells

value: transfection negative control


title: GCs_siYTHDF2_2

value: transfection interference YTHDF2 group


title: GCs_CON_2


title: Well-watered3_59d_rewater1_rep2


title: soleus, Male, B6, Chow, Age 20 Week, Replicate 5


title: 8C_BE_sg_RNA_rep10

city: Beijing

first: Fangnong

last: Lai

state: Beijing

address: Haidian district

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version 1.8
The paired-end reads were aligned with the parameters: -t –q –N 1 –L 25 –X 1000 --no- mixed --no-discordant by Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012). All unmapped reads, non-uniquely mapped reads, and PCR duplicates were removed. For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome. To minimize the batch and cell type variation, RPKM values across the whole genome were further Z-score normalized. To visualize the CUT&RUN signals in the UCSC genome browser, we generated the RPKM values on a 100bp-window base. Peaks were called using MACS v1.4.2 (Zhang et al., 2008) with the parameters nolambda –nomodel. Promoters were defined as ±2.5 kb around the transcription starting sites (TSS). Peaks at least 2.5 kb away from TSSs were defined as distal peaks by BEDTools v2.29.0 (Quinlan and Hall, 2010) .
Assembly: mm9

source_name: Preimplantation embryo

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to males.

extract_protocol:
Cells or embyos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing.

treatment_protocol: Injected with 100 ng/μl BE mRNA and Nr5a2 sgRNA

value: wild type

tag: developmental stage

tag: antibody


title: 8C_BE_sg_RNA_rep14


title: 8C_BE_sg_RNA_rep13


title: Well-watered3_59d_rewater1_rep1


title: Drought6_59d_rep3


title: 8C_BE_sg_RNA_rep6


title: 8C_BE_sg_RNA_rep12


title: 8C_BE_sg_RNA_rep8


title: Drought5_59d_rep3


title: fat, Male, B6, Chow, Age 20 Week, Replicate 6


title: 8C_BE_sg_RNA_rep4


title: 8C_BE_sg_RNA_rep3


title: GCs_siYTHDF2_1


title: Drought6_59d_rep2


title: 8C_BE_sg_RNA_rep7


title: liver, Male, B6, Chow, Age 20 Week, Replicate 5


title: 8C_BE_sg_RNA_rep5


title: Drought5_59d_rep2


title: fat, Male, B6, Chow, Age 20 Week, Replicate 5


title: Drought6_59d_rep1


title: liver, Male, B6, Chow, Age 20 Week, Replicate 4


title: 8C_BE_sg_RNA_rep9


title: 8C_BE_sg_RNA_rep1


title: 8C_BE_sg_RNA_rep11


title: soleus, Male, B6, Chow, Age 20 Week, Replicate 4


title: 8C_sg_RNA_rep8

treatment_protocol: Injected with 100 ng/μl Nr5a2 sgRNA


title: Drought5_59d_rep1


title: 8C_sg_RNA_rep7


title: Well-watered3_59d_rep3


title: 8C_sg_RNA_rep6


title: 8C_BE_sg_RNA_rep2


title: soleus, Male, B6, Chow, Age 20 Week, Replicate 3


title: 8C_sg_RNA_rep5


title: liver, Male, B6, Chow, Age 20 Week, Replicate 3


title: 8C_sg_RNA_rep3


title: fat, Male, B6, Chow, Age 20 Week, Replicate 4


title: 8C_sg_RNA_rep1


title: 8C_sg_RNA_rep2


title: 8C_BE_RNA_rep8

treatment_protocol: Injected with 100 ng/μl BE mRNA


title: 8C_BE_RNA_rep7


title: Drought4_74d_rep3


title: soleus, Male, B6, Chow, Age 20 Week, Replicate 2


title: 8C_BE_RNA_rep6


title: 8C_BE_RNA_rep5


title: liver, Male, B6, Chow, Age 20 Week, Replicate 2


title: fat, Male, B6, Chow, Age 20 Week, Replicate 3


title: 8C_BE_RNA_rep3


title: 8C_BE_RNA_rep4


title: Drought4_74d_rep1


title: soleus, Male, B6, Chow, Age 20 Week, Replicate 1


title: Drought3_74d_rep3


title: 8C_BE_RNA_rep2


title: 8C_BE_RNA_rep1


title: liver, Male, B6, Chow, Age 20 Week, Replicate 1


title: 8C_sg_RNA_rep4


title: 2C_BE_sg_RNA_rep14


title: Drought3_74d_rep2


title: 2C_BE_sg_RNA_rep13


title: Well-watered3_59d_rep2


title: 2C_BE_sg_RNA_rep12


title: Well-watered3_59d_rep1


title: Drought3_74d_rep1


title: 2C_BE_sg_RNA_rep10


title: 2C_BE_sg_RNA_rep11


title: Pancreas, Male, B6, Chow, Age 20 Week, Replicate 6


title: Drought4_74d_rep2


title: Well-watered2_74d_rep3


title: Pancreas, Male, B6, Chow, Age 20 Week, Replicate 5


title: Well-watered2_74d_rep2


title: 2C_BE_sg_RNA_rep9


title: Well-watered2_74d_rep1


title: 2C_BE_sg_RNA_rep8


title: 2C_BE_sg_RNA_rep4


title: Drought2_74d_rep3


title: 2C_BE_sg_RNA_rep7


title: 2C_BE_sg_RNA_rep5


title: Pancreas, Male, B6, Chow, Age 20 Week, Replicate 4


title: 2C_BE_sg_RNA_rep3


title: Pancreas, Male, B6, Chow, Age 20 Week, Replicate 2


title: 2C_BE_sg_RNA_rep2


title: fat, Male, B6, Chow, Age 20 Week, Replicate 2


title: Drought2_74d_rep2


title: Drought2_74d_rep1


title: 2C_BE_sg_RNA_rep1


title: 2C_sg_RNA_rep8


title: 2C_sg_RNA_rep6


title: 2C_sg_RNA_rep7


title: Drought1_74d_rep3


title: 2C_sg_RNA_rep3


title: 2C_sg_RNA_rep5


title: 2C_sg_RNA_rep4


title: 2C_BE_sg_RNA_rep6


title: Drought1_74d_rep2


title: Pancreas, Male, B6, Chow, Age 20 Week, Replicate 3


title: Pancreas, Female, TH, HF, Age 5 Week, Replicate 5

value: F


title: 2C_sg_RNA_rep2


title: Pancreas, Female, TH, HF, Age 5 Week, Replicate 4


title: 2C_BE_RNA_rep7


title: Pancreas, Male, B6, Chow, Age 20 Week, Replicate 1


title: Well-watered1_74d_rep2


title: 2C_BE_RNA_rep8


title: 2C_sg_RNA_rep1


title: Pancreas, Female, TH, HF, Age 5 Week, Replicate 3


title: 2C_BE_RNA_rep6


title: fat, Male, B6, Chow, Age 20 Week, Replicate 1


title: 2C_BE_RNA_rep2


title: 2C_BE_RNA_rep4


title: 2C_BE_RNA_rep5


title: 2C_BE_RNA_rep3


title: Pancreas, Female, TH, HF, Age 5 Week, Replicate 1


title: Drought6_56d_rep3


title: Pancreas, Female, TH, HF, Age 5 Week, Replicate 2


title: 2C_BE_RNA_rep1


title: Drought6_56d_rep2


title: 8C_Nr5a2_KD_ATAC_rep1

library_source: genomic

molecule: genomic DNA

extract_protocol:
Cells or embyos were lysed in wash buffer.
The ATAC-seq procedure was performed as previously described (Wu et al. 2018). Briefly, cells were transferred into 6 μl of lysis buffer [10 mM tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.02% digitonin) in ice for 10 min. The ATAC reaction was performed by adding 4 μl of ddH2O, 4 μl of 5× TTBL, and 5 μl TTE mix V5 (Vazyme Biotech Co.,Ltd, catalog no. TD502) at 37°C for 30 min and then stopped by adding 5 μl of 5× TS stop buffer at room temperature for 5 min. DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng of carrier RNA and 103 μl of tris-EDTA. Then, DNA was PCR-amplified with 10 μl of index (Vazyme Biotech Co.,Ltd, catalog no. TD202), 10 μl of 5× TAB and 1 μl tris-acetate-EDTA (Vazyme Biotech Co.,Ltd, catalog no. TD502) with the program of 72°C for 3 min, 98°C for 30 s, (98°C for 15 s, 60°C for 30 s, and 72°C for 3 min) with 18 cycles, and 72°C for 5 min.

treatment_protocol: Injected with 5 μM  Nr5a2 siRNA separately


title: fat, Female, TH, HF, Age 5 Week, Replicate 6


title: 8C_Nr5a2_NC_ATAC_rep2

treatment_protocol: Injected with 5 μM NC siRNA


title: Drought6_56d_rep1


title: Well-watered1_74d_rep1


title: Well-watered1_74d_rep3


title: 8C_Nr5a2_KD_ATAC_rep2


title: Pancreas, Female, TH, HF, Age 5 Week, Replicate 6


title: Drought1_74d_rep1


title: fat, Female, TH, HF, Age 5 Week, Replicate 5


title: 8C_Nr5a2_NC_ATAC_rep1


title: fat, Female, TH, HF, Age 5 Week, Replicate 3


title: Drought5_56d_rep2


title: fat, Female, TH, HF, Age 5 Week, Replicate 2


title: Well-watered3_56d_rep3


title: 2C_Nr5a2_KD_ATAC_rep2


title: Drought5_56d_rep1


title: soleus, Female, TH, HF, Age 5 Week, Replicate 7


title: fat, Female, TH, HF, Age 5 Week, Replicate 1


title: 2C_Nr5a2_NC_RNA_rep2

treatment_protocol: Injected with 20 μM NC siRNA


title: 2C_Nr5a2_NC_ATAC_rep1


title: 2C_Nr5a2_NC_ATAC_rep2


title: 2C_Nr5a2_KD_RNA_rep1

treatment_protocol: Injected with 20 μM Nr5a2 siRNA


title: soleus, Female, TH, HF, Age 5 Week, Replicate 6


title: Drought6_53d_rep3


title: 2C_Nr5a2_NC_ATAC_rep3


title: Well-watered3_56d_rep2


title: 8C_Nr1h3_KD_rep1

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours_x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000_㽝㽛므羰_x0000__x0000__x0000__x0000__x0000_

treatment_protocol: Injected with 5 μM  Nr1h3 siRNA separately


title: 8C_Nr2c2_KD_rep2

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours_x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0004__x0000__x0000__x0000_므羰_x0000__x0000__x0000__x0000__x0000_

extract_protocol:
Cells or embyos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before be_x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0004_ആ߻倀므羰_x0000__x0000__x0000__x0000__x0000_饒୥

treatment_protocol: Injected with 5 μM  Nr2c2 siRNA separately


title: liver, Female, TH, HF, Age 5 Week, Replicate 6


title: fat, Female, TH, HF, Age 5 Week, Replicate 4


title: 2C_Nr5a2_KD_RNA_rep2


title: Drought5_56d_rep3


title: 8C_Rarg_KD_rep2

treatment_protocol: Injected with 5 μM  Rarg siRNA separately


title: 2C_Nr5a2_KD_ATAC_rep1


title: 2C_Nr5a2_KD_ATAC_rep3


title: 2C_Nr5a2_NC_RNA_rep1


title: 8C_Nr1h3_KD_rep2


title: Drought6_53d_rep2


title: soleus, Female, TH, HF, Age 5 Week, Replicate 5


title: 8C_Nr5a2_KD_rep2


title: 8C_Nr5a2_KD_rep1


title: Drought5_53d_rep3


title: Well-watered3_56d_rep1


title: liver, Female, TH, HF, Age 5 Week, Replicate 5


title: Drought5_53d_rep2


title: soleus, Female, TH, HF, Age 5 Week, Replicate 4


title: 8C_1NR_NC_rep2


title: 8C_1NR_NC_rep1


title: 8C_Nr2c2_KD_rep1


title: 8C_Nr5a2_Rarg_Nr1h3_KD_rep2

treatment_protocol: Injected with 5 μM  Nr5a2/Rarg/Nr1h3 siRNA separately


title: liver, Female, TH, HF, Age 5 Week, Replicate 4


title: 8C_Nr5a2_Rarg_Nr1h3_KD_rep1


title: 8C_Nr5a2_Rarg_Nr2c2_KD_rep2

treatment_protocol: Injected with 5 μM  Nr5a2/Rarg/Nr2c2 siRNA separately


title: Drought5_53d_rep1


title: 8C_Nr5a2_Nr1h3_Nr2c2_KD_rep2

treatment_protocol: Injected with 5 μM  Nr5a2/Nr1h3/Nr2c2 siRNA separately


title: Drought6_53d_rep1


title: 8C_Rarg_Nr1h3_Nr2c2_KD_rep2

treatment_protocol: Injected with 5 μM  Rarg/Nr1h3/Nr2c2 siRNA separately


title: 8C_Rarg_KD_rep1


title: soleus, Female, TH, HF, Age 5 Week, Replicate 3


title: 8C_Nr5a2_Rarg_Nr2c2_KD_rep1


title: Well-watered3_53d_rep3


title: Well-watered3_53d_rep2


title: soleus, Female, TH, HF, Age 5 Week, Replicate 2


title: 8C_3NR_NC_rep2

treatment_protocol: Injected with 15 μM NC siRNA


title: liver, Female, TH, HF, Age 5 Week, Replicate 2

treatment_protocol: At 4 weeks of age, male and female TALLYHO/Jng (TH) and C57BL/6J (B6) mice were weaned onto either standard chow or high fat diets and maintained on the respective diets. After 1 and 16 weeks of feeding (5 and 20 weeks of age), mice were euthanized by CO2 inhalation followed by cervical dislocation and exsanguination via cardiac puncture. Tissues including liver, gonadal fat, soleus muscle, and pancreas were then collected for RNA isolation.


title: soleus, Female, TH, HF, Age 5 Week, Replicate 1


title: Drought4_68d_rep3

treatment_protocol: The water level in each pot was maintained at 6 cm above the bottom of the pot under WW conditions. Drought stress was initiated at each indicated days after sowing by withdrawing water supply.


title: 8C_Nr5a2_Nr1h3_Nr2c2_KD_rep1


title: 8C_Nr5a2_Rarg_Nr1h3_Nr2c2_KD_rep1

treatment_protocol: Injected with 5 μM  Nr5a2/Rarg/Nr1h3/Nr2c2 siRNA separately


title: 8C_Nr5a2_Rarg_Nr1h3_Nr2c2_KD_rep2


title: Drought4_68d_rep1


title: 8C_4NR_NC_rep1


title: Drought4_68d_rep2


title: Well-watered3_53d_rep1


title: 4C_Nr5a2_Rarg_Nr1h3_Nr2c2_KD_rep2


title: liver, Female, TH, HF, Age 5 Week, Replicate 3


title: Pancreas, Female, TH, HF, Age 20 Week, Replicate 6


title: 8C_Rarg_Nr1h3_Nr2c2_KD_rep1


title: Pancreas, Female, TH, HF, Age 20 Week, Replicate 5


title: 4C_4NR_NC_rep2


title: Drought3_68d_rep3


title: 100k_NR5A2_ChIP

source_name: serum mESC

growth_protocol: ES cells were cultured in non-adhesive bacterial dishes using ES culture medium minus LIF for 4 days. Then retinoic acid (RA) (Sigma Cat. R2625) was added in to medium to the final concentration of 2ug/ml. Medium was changed every day. On the 5th day of adding RA, embryonic bodies were dissociated by 0.25% Trypsin-EDTA (Gibco Cat. 25200-056) and plated to poly-L-ornithine (Sigma Cat. P3655) and Laminin (Invitrogen Cat. 23017-015) pre-coated dish. Cells were cultured in DMEM/F-12 (Gibco Cat. 11330-032) with B27 (Life tech. Cat. 17504-044) and were incubated for two days. The medium was switched to BME (Gibco, Cat. 21010-046) with B27 for another two days. Differentiated neurons were then harvested for subsequent analyses.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication to obtain fragments 200–2000 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.


title: 8C_3NR_NC_rep1


title: 4C_4NR_NC_rep1


title: Pancreas, Female, TH, HF, Age 20 Week, Replicate 4


title: 4C_Nr5a2_Rarg_Nr1h3_Nr2c2_KD_rep1


title: Drought3_68d_rep2


title: Pancreas, Female, TH, HF, Age 20 Week, Replicate 3


title: 100k_Input_ChIP


title: liver, Female, TH, HF, Age 5 Week, Replicate 1


title: 9000_mESC_WT_NR5A2_CR

data_processing:
Basecalls performed using CASAVA version 1.8
The paired-end reads were aligned with the parameters: -t –q –N 1 –L 25 –X 1000 --no- mixed --no-discordant by Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012). All unmapped reads, non-uniquely mapped reads, and PCR duplicates were removed. For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome. To minimize the batch and cell type variation, RPKM values across the whole genome were further Z-score normalized. To visualize the CUT&RUN signals in the UCSC genome browser, we generated the RPKM values on a 100bp-window base. Peaks were called using MACS v1.4.2 (Zhang et al., 2008) with the parameters nolambda –nomodel. Promoters were defined as ±2.5 kb around the transcription starting sites (TSS). Peaks at least 2.5 kb away from TSSs were defined as distal peaks by BEDTools v2.29.0 (Quinlan and Hall, 2010) .
Assembly: mm9
Library strategy: CUT&RUN

growth_protocol: serum mES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03), leukemia inhibiting factor (LIF) (Millipore Cat. GSE1107), penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), and non-essential amino acids (Gibco Cat. 25-025-CIR).

extract_protocol:
Cells or embyos were lysed in wash buffer.
CUT&RUN was conducted following the published protocol (Skene et al., 2018). ESCs or embryos with zona pellucida removed were transferred into 0.2mL conventional, non-low-binding PCR tube (Axygen). The samples were resuspended by 60μL washing buffer (HEPES-KOH, pH = 7.5, 20mM; NaCl, 150mM; Spermidine, 0.5mM and with Roche complete protease inhibitor. Concanavalin-coated magnetic beads (Polyscience, 86057) 10-20μL for each sample were gently washed, resuspended by binding buffer (HEPES-KOH, pH = 7.9, 20mM; KCl, 10mM; CaCl2, 1mM; MnCl2, 1mM) and carefully added to the samples. The samples were then incubated at 23°C for 10 mins on Thermomixer (Eppendorf) at 400 rpm. The samples were then held at the magnetic stand to carefully aspirate buffer and were resuspended by 75μL antibody buffer (washing buffer plus 0.01% digitonin; EDTA, pH = 8.0, 2mM) with NR5A2 antibody (R&D, P-H2325-00) diluted at ratio of 1:100. The samples were then incubated at 4°C on Thermomixer for 3 hours at 400 rpm. After that, the samples were held at the magnetic stand and transfer to antibody buffer with rabbit anti-mouse IgG (Abcam, ab46540) diluted at ratio of 1:100. After that he samples were washed by 200μL dig washing buffer (washing buffer plus 0.01% digitonin) for once and 100μL for a second time. The samples were then resuspended by 75 μL dig washing buffer with pA-MNase (to a final concentration of 700ng/mL), and incubated at 4°C on Thermomixer for 1 hour at 400 rpm. The samples were washed by 200μL dig washing buffer twice at the magnetic stand. The samples were resuspended by 100μL dig washing buffer and balanced on ice for 2 mins. Targeted digestion was performed on ice by adding 2μL 100mM CaCl2 for 30 mins, and reaction was stopped by adding 100μL 2 × stop buffer (NaCl, 340mM; EDTA, pH = 8.0, 20mM; EGTA, pH = 8.0, 4mM; RNase A, 50μg/mL; glycogen, 100μg/mL) and fully vortexed. The samples were then incubated at 37°C of 30 mins for fragment releasing. The supernatants were purified by phenol-chloroform followed by ethanol purification.


title: Drought3_68d_rep1


title: Well-watered2_68d_rep3


title: 2000_mESC_NR5A2_CR


title: 1000_mESC_NR5A2_CR


title: Pancreas, Female, TH, HF, Age 20 Week, Replicate 1


title: 9000_mESC_NR5A2KO_NR5A2_CR

value: Nr5a2 KO


title: Well-watered2_68d_rep2


title: 8C_4NR_NC_rep2


title: soleus, Female, TH, HF, Age 20 Week, Replicate 6


title: Pancreas, Female, TH, HF, Age 20 Week, Replicate 2


title: Drought2_68d_rep3


title: liver, Female, TH, HF, Age 20 Week, Replicate 6


title: Drought2_68d_rep2


title: Drought2_68d_rep1


title: fat, Female, TH, HF, Age 20 Week, Replicate 6


title: ChIP C2C12_KO_1_D5_MR_rep1

city: Durham

first: Yudong

last: Sun

state: NC

address: 308 Research Drive

institute: Duke University

data_processing:
Fastq files were processed with the nf-core/chipseq pipeline using default parameters (genome: GRCm38, macs_gsize: 2652783500).
Assembly: GRCm38
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

extract_protocol:
C2C12 cells were fixed in formaldehyde. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). Extrapolation to the original chromatin volume allowed determination of the total chromatin yield.
Illumina sequencing libraries (a custom type, using the same paired read adapter oligonucleotides30) were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NovaSeq 6000 (75 nt reads, single end). An aliquot of chromatin, 30 ug chromatin (750 ng of Drosophila chromatin for spike-in for H3K36me329) was precleared with protein G agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4ul of H3K36me3 (Active Motif cat# 61101, lot# 22264149) and 0.4ug of antibody against H2Av (Active Motif cat# 61686). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.

tag: cell line

value: mouse myoblast

tag: chip antibody

value: H3K36me3 (Active Motif #61101)


title: ChIP C2C12_WT_D5_MR_rep2


title: ChIP C2C12_WT_D5_CTL_rep2


title: ChIP C2C12_KO_1_D5_CTL_rep1


title: ChIP C2C12_WT_D5_MR_rep1


title: ChIP C2C12_KO_2_D5_MR_rep1


title: ChIP C2C12_KO_2_D5_CTL_rep1


title: soleus, Female, TH, HF, Age 20 Week, Replicate 5

value: soleus


title: ChIP C2C12_KO_2_D1_MR_rep1


title: ChIP C2C12_WT_D5_CTL_rep1


title: ChIP C2C12_KO_1_D1_MR_rep1


title: Drought1_68d_rep3


title: ChIP C2C12_KO_2_D1_CTL_rep1


title: liver, Female, TH, HF, Age 20 Week, Replicate 5


title: fat, Female, TH, HF, Age 20 Week, Replicate 5


title: ChIP C2C12_WT_D1_MR_rep2


title: ChIP C2C12_KO_1_D1_CTL_rep1


title: ChIP C2C12_WT_D1_MR_rep1


title: ChIP C2C12_WT_D1_CTL_rep2


title: ChIP C2C12_WT_D1_CTL_rep1


title: soleus, Female, TH, HF, Age 20 Week, Replicate 4


title: Drought1_68d_rep1


title: Well-watered1_68d_rep3


title: Well-watered2_68d_rep1


title: liver, Female, TH, HF, Age 20 Week, Replicate 4


title: fat, Female, TH, HF, Age 20 Week, Replicate 4


title: Well-watered1_68d_rep2


title: Well-watered1_68d_rep1


title: Drought6_50d_rep3


title: ChIP C2C12_WT_D0_rep2


title: soleus, Female, TH, HF, Age 20 Week, Replicate 3


title: Drought6_50d_rep2


title: Drought1_68d_rep2


title: liver, Female, TH, HF, Age 20 Week, Replicate 3


title: fat, Female, TH, HF, Age 20 Week, Replicate 3


title: Drought6_50d_rep1


title: Drought5_50d_rep3


title: soleus, Female, TH, HF, Age 20 Week, Replicate 2


title: Drought5_50d_rep2


title: liver, Female, TH, HF, Age 20 Week, Replicate 2


title: ChIP C2C12_WT_KO_Input


title: fat, Female, TH, HF, Age 20 Week, Replicate 2


title: Drought5_50d_rep1


title: Well-watered3_50d_rep3


title: Well-watered3_50d_rep2


title: liver, Female, TH, HF, Age 20 Week, Replicate 1


title: soleus, Female, TH, HF, Age 20 Week, Replicate 1


title: fat, Female, TH, HF, Age 20 Week, Replicate 1


title: ChIP C2C12_WT_D0_rep1


title: Pancreas, Female, TH, Chow, Age 5 Week, Replicate 7


title: ChIP C2C12_KO_1_D0_rep1


title: ATAC C2C12_KO_2_D5_CTL_rep1

data_processing:
Fastq files were processed with the nf-core/atacseq pipeline using default parameters (genome: GRCm38, macs_gsize: 2652783500).
Assembly: GRCm38
Supplementary files format and content: bigWig, broadPeak

source_name: ATAC C2C12

extract_protocol:
Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif).
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using Qubit (Invitrogen) and TapeStation (Agilent), then sequenced with PE42 sequencing on the NovaSeq 6000 sequencer (Illumina).

value: KO


title: ATAC C2C12_KO_2_D5_MR_rep1


title: ATAC C2C12_WT_D1_CTL_rep2

value: WT


title: ATAC C2C12_WT_D5_CTL_rep1


title: ATAC C2C12_WT_D5_CTL_rep2


title: ATAC C2C12_KO_2_D0_rep1


title: ATAC C2C12_KO_1_D1_MR_rep1


title: ATAC C2C12_KO_1_D0_rep1


title: ATAC C2C12_KO_1_D1_CTL_rep1


title: ATAC C2C12_KO_2_D1_CTL_rep1


title: ATAC C2C12_KO_2_D1_MR_rep1


title: ATAC C2C12_WT_D5_MR_rep2


title: ATAC C2C12_KO_1_D5_MR_rep1


title: ATAC C2C12_WT_D1_MR_rep1


title: ATAC C2C12_WT_D1_MR_rep2


title: ChIP C2C12_KO_2_D0_rep1


title: ATAC C2C12_WT_D1_CTL_rep1


title: ATAC C2C12_KO_1_D5_CTL_rep1


title: Drought4_65d_rep3


title: ATAC C2C12_WT_D0_rep2


title: ATAC C2C12_WT_D0_rep1


title: Well-watered3_50d_rep1


title: Drought4_65d_rep2


title: ATAC C2C12_WT_D5_MR_rep1


title: Pancreas, Female, TH, Chow, Age 5 Week, Replicate 5

value: TH

value: Chow


title: Drought3_65d_rep2

value: Nipponbare


title: Pancreas, Female, TH, Chow, Age 5 Week, Replicate 1

value: Pancreas


title: Pancreas, Female, TH, Chow, Age 5 Week, Replicate 4


title: Drought3_65d_rep3


title: Drought3_65d_rep1


title: Pancreas, Female, TH, Chow, Age 5 Week, Replicate 2


title: Well-watered2_65d_rep3


title: Pancreas, Female, TH, Chow, Age 5 Week, Replicate 3


title: Well-watered2_65d_rep2


title: soleus, Female, TH, Chow, Age 5 Week, Replicate 6


title: NG2ko_Norm03

city: Chicago

first: David

middle: A

last: Reed

state: IL

address: 801 South Paulina Street

department: Department of Oral Biology

institute: University of Illinois at Chicago

description: Data analysis published in Reed et al, "NG2/CSPG4 attenuates motility in mandibular fibrochondrocyte under serum starvation conditions" in Frontiers in Cell and Developmental Biology

data_processing:
For bioinformatics analysis, in house scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases (56). Then sequence quality was verified using FastQC
HISAT2 (57) was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/.
The mapped reads of each sample were assembled using StringTie (58). Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie (58) and edgeR (59) was used to estimate the expression levels of all transcripts

molecule: polyA RNA

source_name: mandiibular condylar cartilage

growth_protocol: Primary cells isolated from mandibular condylar cartilage of 10-14 day old mice, digested overnight in collagenase, and plated. RNA collected at passage 4

extract_protocol:
QIAGEN RNEasy kit
a Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation proto
RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification
After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip
. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system

treatment_protocol: NORMAL - None, normal growth conditions in AMEM, heat inactivated FBS, L-Glut, Pen, and Plasmocin; Serum Starvation - Optimem with L-Glut, Pen, and Plasmocin

value: mandiibular condylar cartilage

value: primary

value: mandibualr fibrochondrocyte

value: NG2/CSPG4 knockout

value: Optimem Serum Free


title: NG2ko_Norm01


title: Well-watered2_65d_rep1


title: Pancreas, Female, TH, Chow, Age 5 Week, Replicate 6


title: hippocampus 1,LPS+VEGFC, Day3

city: Nanjing

first: Hongquan

last: Dong

address: 300 Guangzhou Road

institute: Nanjing Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads fIndex of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling norma
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected
GATK2 (v3.7) software was used to perform SNP calling.rMATS(3.2.5) software was used to analysis the AS event.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for exch sample

source_name: brain

extract_protocol:
RNA degradation and contamination was monitored on 1% agaros.RNA purity was checked using the NanoPhotometer®spectrophotometer(IMPLEN, CA, USA)RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies,CA,USA).A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: brain

value: LPS ip + AAV1-VEGF-C icm


title: hippocampus 2,LPS+VEGFC, Day3


title: hippocampus 3, LPS, Day3

value: LPS ip


title: Drought4_65d_rep1


title: hippocampus 1, LPS, Day3


title: NG2_Opti03

value: Norm AMEM growth conditions


title: liver, Female, TH, Chow, Age 5 Week, Replicate 6

value: liver

value: F


title: fat, Female, TH, Chow, Age 5 Week, Replicate 6

value: fat


title: fat, Female, TH, Chow, Age 5 Week, Replicate 5


title: Drought6_47d_rep3


title: Drought6_47d_rep2


title: Mouse aortic endothelial cell_Female #3

city: Cleveland

first: Olga

last: Cherepanova

state: OHIO

address: 9620 Carnegie Ave N Bldg

department: Cardiovascular and Metabolic Science

institute: Cleveland Clinic Lerner Research Institute

data_processing:
The genome was bulit using Hisat2 V2.0.5
FeatureCounts v1.5--p3 was used to count the read numbers mapped to each gene.
Supplementary files format and content: tab-dekunuted text file includes raw counts for each sample.

source_name: MAEC

growth_protocol: Mouse aotic endothelial cells were maintained in F-12 media with 20% fetal bovine serum (FBS), antibiotics, heparin, and endothelial cell growth factors in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Tizol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers., followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: no treatment

value: MAEC

value: Endothelial cell

value: Wild type

tag: gender

value: female


title: NG2_Opti02


title: Mouse aortic endothelial cell_Male #3

value: male


title: Mouse aortic endothelial cell_Male #1


title: Mouse aortic endothelial cell_Female #1


title: NG2ko_Norm02

value: mandiibular condylar cartilage


title: hippocampus 2, LPS, Day3


title: Drought6_47d_rep1

value: Nipponbare


title: Mouse aortic endothelial cell_Male #2


title: Mouse aortic endothelial cell_Female #2


title: Cont_Opti03

value: primary

value: mandibualr fibrochondrocyte

value: wild type


title: NG2_Opti01

value: NG2/CSPG4 knockout


title: hippocampus 3,LPS+VEGFC, Day3

value: brain

value: LPS ip + AAV1-VEGF-C icm


title: Cont_Norm03

value: Norm AMEM growth conditions


title: Cont_Opti01

value: Optimem Serum Free


title: soleus, Female, TH, Chow, Age 5 Week, Replicate 5

value: soleus

value: F

value: TH

value: Chow


title: Cont_Norm02


title: fat, Female, TH, Chow, Age 5 Week, Replicate 4

value: fat


title: liver, Female, TH, Chow, Age 5 Week, Replicate 5

value: liver


title: Cont_Norm01


title: soleus, Female, TH, Chow, Age 5 Week, Replicate 4


title: Drought5_47d_rep2


title: WT-HSV

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

description: BMDMs were collected for total RNA extraction with HSV infection for 12 hours.

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to mouse mm10 genome using subread, which produced the BAM type file directly.
The featureCounts and TEtranscripts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The GFOLD software was used to identify the differantially expressed genes.
Assembly: UCSC mm10 genome was used as reference genome.
Supplementary files format and content: Excel spreadsheet file includes raw genes and TEs counts for each Sample
Supplementary files format and content: Excel spreadsheet file includes the FPKM value for each sample.

source_name: bone marrow

growth_protocol: BMDMs were cultured in DMEM medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2..

extract_protocol:
Total RNA was extracted using Trizol reagent (TIANGEN). 1.5 ug of total RNA was used for the construction of sequencing libraries.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: BMDMs were infected by VSV and HSV for 12 hours.

value: bone marrow

value: Bone Marrow Derived Macrophages

value: wt

value: HSV


title: Drought5_47d_rep1

value: Nipponbare


title: liver, Female, TH, Chow, Age 5 Week, Replicate 4


title: WT-VSV

description: BMDMs were collected for total RNA extraction with VSV infection for 12 hours.

value: VSV


title: WT-MOCK

description: BMDMs were collected for total RNA extraction without infection.

value: MOCK


title: Well-watered3_47d_rep2


title: fat, Female, TH, Chow, Age 5 Week, Replicate 3


title: 85- vehicle 35k

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic single cell

data_processing:
CellRanger count (v7.0.1) : default parameters
Assembly: GRCm39 (mm39)
Supplementary files format and content: raw_feature_bc_matrix

source_name: PDAC tumors

extract_protocol:
Chromium Next GEM Single Cell 3' Kit v3.1, PN-1000268; Chromium Next GEM Chip G Single Cell Kit, PN-1000120; Dual Index Kit TT Set A, PN-1000215; and the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) user guide
10x Genomics single nuclei RNA-seq

treatment_protocol: PDAC tumor-bearing mice were treated for 2 weeks with 60 mg/kg Neratinib or vehicle

value: PDAC tumors

value: Vehicle


title: 94-neratinib 35k

value: Neratinib


title: 76- vehicle 35k


title: 78-neratinib 35k


title: 80-neratinib 35k


title: Well-watered3_47d_rep1


title: Drought5_47d_rep3


title: soleus, Female, TH, Chow, Age 5 Week, Replicate 3


title: Drought4_62d_rep3


title: 79-vehicle 35K


title: 84-neratinib 35k


title: 88-vehicle 35K


title: sample.621

city: St. Louis

first: Abhirami Kannan

last: Iyer

state: MISSOURI

address: 425 South euclid ave, BJC Institute of Health, Room 9202

department: Psychiatry

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions. KEGG and WikiPathways (species: Mus musculus, year queried: 2019) were used to derive functional annotations of the differentially expressed genes into pathways.
Assembly: Mouse Ensembl GRCm38.76

source_name: spinal cord

extract_protocol:
Total RNA was extracted from harvested mouse tissues using RNeasy Mini Kit (Qiagen, 74104)
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Control or Atp1a2-specific ASOs were delivered centrally via ICV single bolus injection. The mouse was allowed to recover on a heated pad until ambulatory with most mice recovering 20 minutes to 2 hours after ICV injection. The mice were examined everyday thereafter for pain, discomfort, and infections. All ICV injections were performed in a blinded manner such that the person processing the tissues and carrying out downstream analyses was blinded to the agent administered in each mouse until all the experimental analyses were completed.

value: B6SJL-Tg (SOD1*G93A)1Gur/J

value: control ASO

tag: aso concentration


title: sample.558


title: Cont_Opti02

value: mandiibular condylar cartilage

value: primary

value: mandibualr fibrochondrocyte

value: wild type

value: Optimem Serum Free


title: soleus, Female, TH, Chow, Age 5 Week, Replicate 2

value: soleus

value: F

value: TH

value: Chow


title: fat, Female, TH, Chow, Age 5 Week, Replicate 2

value: fat


title: Drought4_62d_rep2

value: Nipponbare


title: Drought4_62d_rep1


title: sample.656


title: sample.648


title: Well-watered3_47d_rep3


title: liver, Female, TH, Chow, Age 5 Week, Replicate 2

value: liver


title: Drought3_62d_rep3


title: liver, Female, TH, Chow, Age 5 Week, Replicate 3


title: sample.748


title: sample.582

value: Atp1a2 ASO3


title: sample.740


title: Drought3_62d_rep1


title: Drought3_62d_rep2


title: liver, Female, TH, Chow, Age 5 Week, Replicate 1


title: soleus, Female, TH, Chow, Age 5 Week, Replicate 1


title: sample.618


title: sample.633


title: fat, Female, TH, Chow, Age 5 Week, Replicate 1


title: sample.626


title: sample.718


title: Well-watered2_62d_rep3


title: Pancreas, Female, TH, Chow, Age 20 Week, Replicate 7

value: Pancreas


title: sample.726


title: Well-watered2_62d_rep2


title: sample.622


title: sample.599


title: Well-watered2_62d_rep1


title: sample.689


title: Pancreas, Female, TH, Chow, Age 20 Week, Replicate 6


title: Drought2_62d_rep3


title: sample.734


title: sample.706


title: sample.645

value: Atp1a2 ASO1


title: sample.712

value: B6SJL-Tg (SOD1*G93A)1Gur/J


title: Drought2_62d_rep2


title: Pancreas, Female, TH, Chow, Age 20 Week, Replicate 4


title: sample.703


title: Pancreas, Female, TH, Chow, Age 20 Week, Replicate 8


title: sample.630


title: Drought2_62d_rep1


title: Pancreas, Female, TH, Chow, Age 20 Week, Replicate 3


title: Drought1_62d_rep3


title: sample.713


title: sample.700


title: Pancreas, Female, TH, Chow, Age 20 Week, Replicate 2


title: OC, Impdh2 LysM-cKO, R40D3, rep2

city: Wuhan

first: cheng

last: xu

state: Hubei

address: Sanjiaohu Road

institute: Jianghan University

description: Impdh2 LysM-cKO_counts rep2.txt

data_processing:
The quality of raw data was evaluated using FastQC (v0.11.2)
Sequencing reads were trimmed for adaptor/low-quality sequence using Trimmomatic (v0.36)
Clean data were aligned to reference genome via software Hisat2 (v2.1.0)
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million mapped fragments
Differential expression analysis of two conditions/groups was performed using the DESeq2 (v1.12.4)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes counts for Impdh2 WT and Impdh2 Prx-cKO samples from forelimbs
Supplementary files format and content: tab-delimited text file includes counts for  Impdh2 WT and Impdh2 LysM-cKO samples from osteoclasts

source_name: osteoclast

growth_protocol: For forlimbs, E12.5 embyros form Wt and Impdh2 Prx-cKO were harvested; for osteoclast differentiation, mouse bone marrow cells from Wt and  Impdh2 LysM-cKO mice were extracted and cultured for 3 days in α-MEM medium with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and L929 cell supernatant, which contained the equivalent of 20 ng/ml of murine rM-CSF and was used as a source of M-CSF.

extract_protocol:
Total RNA was extracted from the samples using the TRIzol reagent.
RNA libraries for sequencing were prepared using the Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® according to the manufacturer’s instructions.

treatment_protocol: For osteoclast  differentiation, the attached bone marrow–derived macrophages (BMMs) were scraped, and 4.5×104 cells/cm2 were seeded in α-MEM medium with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and CM for overnight, and then stimulated by 40 ng/ml RNAKL and CM.

value: osteoclast

value: Impdh2 LysM-cKO

value: osteoclast differentiation


title: OC, Impdh2 LysM-cKO, R0D3, rep2

description: Impdh2 LysM-cKO_counts rep2.txt


title: OC, Impdh2 Wt, R40D3, rep2

description: Impdh2 LysM-cKO_counts rep2.txt

value: Wt


title: Drought1_62d_rep1


title: Drought1_62d_rep2


title: OC, Impdh2 Wt, R0D3, rep1

description: Impdh2 LysM-cKO_counts rep1.txt


title: soleus, Female, TH, Chow, Age 20 Week, Replicate 6

extract_protocol:
Total RNA was isolated from the tissue using RNeasy Plus Universal Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
All RNA samples were assessed using the Bioanalyzer 2100 and quantified using the Thermo Fisher Qubit RNA assay. Each RNA sample with a RIN value above 8 and a quantity of 1000ng was utilized to generate a Poly(A)-based RNAseq library following the Illumina TruSeq stranded mRNA protocol. Briefly, the poly(A) RNAs were purified using oligo dT magnetic beads and were then fragmented with divalent cations, followed by reverse transcription into cDNA. The Illumina paired-end oligo adapters were ligated to the cDNA fragments, and the RNAseq libraries were amplified using PCR. The finished libraries were purified and analyzed on an Agilent Bioanalyzer 2100, revealing an average library size ranging from 285 to 300 base pairs. To determine the quantity of these libraries, they were further measured using the Thermo Fisher Qubit HS dsDNA assay.


title: Well-watered1_62d_rep3

extract_protocol:
Total RNA was extracted using TRIzol RNA Isolation Reagents (Thermo Fisher) according to manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional mRNA-seq kit (New England Biolabs)


title: Pancreas, Female, TH, Chow, Age 20 Week, Replicate 5


title: sample.652


title: OC, Impdh2 Wt, R40D3, rep1

description: Impdh2 LysM-cKO_counts rep1.txt


title: liver, Female, TH, Chow, Age 20 Week, Replicate 6


title: OC, Impdh2 LysM-cKO, R40D3, rep1

description: Impdh2 LysM-cKO_counts rep1.txt


title: Well-watered1_62d_rep2


title: fat, Female, TH, Chow, Age 20 Week, Replicate 6


title: Forelimbs, Impdh2 Prx-cKO, E12.5, rep1

description: Impdh2 Prx-cKO_counts.txt

source_name: Forelimbs

value: Forelimbs

value: Impdh2 Prx-cKO


title: Forelimbs, Impdh2 Prx-cKO, E12.5, rep2

description: Impdh2 Prx-cKO_counts.txt


title: Well-watered1_62d_rep1


title: OC, Impdh2 Wt, R0D3, rep2

description: Impdh2 LysM-cKO_counts rep2.txt


title: Drought6_44d_rep3


title: Forelimbs, Impdh2 Wt, E12.5, rep2

description: Impdh2 Prx-cKO_counts.txt


title: Pancreas, Female, TH, Chow, Age 20 Week, Replicate 1


title: soleus, Female, TH, Chow, Age 20 Week, Replicate 5

value: soleus


title: Forelimbs, Impdh2 Wt, E12.5, rep1

description: Impdh2 Prx-cKO_counts.txt


title: 2A_53179_V_caf

data_processing:
Estimated transcript counts were counted using Salmon (version 1.9.0)
Assembly: GRCm39 (mm39)
Supplementary files format and content: Raw count data in tab-delimited text format.

source_name: FACS sorted PDPN+ cells from PDAC tumor

extract_protocol:
Samples were collected in 1 mL of TRIzol Reagent and stored at -80C. The RNA was extracted using the RNeasy Micro kit (74004; Qiagen)
For the PCR steps, we performed 14 cDNA PCR cycles for samples <1ng; 11 cDNA PCR cycles for samples at <10ng; and
8 cDNA PCR cycles for samples between >10ng an <100ng.For the final PCR step, we performed 9 PCR cycles for samples <10ng and
6 PCR cycles for samples >10ng.
the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (E6420S) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pair) (E6440S)

value: FACS sorted PDPN+ cells from PDAC tumor

value: vehicle


title: 6B_53192_V_epi

source_name: FACS sorted EpCAM+ cells from PDAC tumor


title: Drought6_44d_rep2


title: 10B_53184_N_epi

value: FACS sorted EpCAM+ cells from PDAC tumor

value: neratinib


title: OC, Impdh2 LysM-cKO, R0D3, rep1

description: Impdh2 LysM-cKO_counts rep1.txt


title: 3A_53185_V_caf


title: 8A_53184_N_caf


title: Drought6_44d_rep1

value: Nipponbare


title: 7B_53178_N_epi


title: liver, Female, TH, Chow, Age 20 Week, Replicate 5

value: liver

value: F

value: TH

value: Chow


title: fat, Female, TH, Chow, Age 20 Week, Replicate 5

source_name: fat

value: fat


title: 7A_53180_N_caf


title: liver, Female, TH, Chow, Age 20 Week, Replicate 4


title: Drought5_44d_rep3


title: fat, Female, TH, Chow, Age 20 Week, Replicate 4


title: 2B_53176_V_epi


title: 12B_53193_N_epi


title: Drought5_44d_rep1


title: Well-watered3_44d_rep3


title: 8B_53180_N_epi


title: 4B_53185_V_epi


title: 6A_53178_N_caf


title: 1B_53175_V_epi


title: 4A_53188_V_caf


title: liver, Female, TH, Chow, Age 20 Week, Replicate 3


title: Well-watered3_44d_rep2


title: 3B_53179_V_epi


title: soleus, Female, TH, Chow, Age 20 Week, Replicate 4

source_name: soleus


title: Well-watered3_44d_rep1


title: 5B_53188_V_epi


title: 9A_53194_N_caf


title: fat, Female, TH, Chow, Age 20 Week, Replicate 3


title: soleus, Female, TH, Chow, Age 20 Week, Replicate 2


title: Drought4_59d_rep3


title: 13C_52702_KO_epi

data_processing:
Estimated transcript counts were counted using Salmon (version 1.9.0)
Assembly: GRCm39 (mm39)
Supplementary files format and content: Raw count data in tab-delimited salmon file

source_name: T6-LOH organoids

value: T6-LOH organoids

value: epithelial cells from PDAC tumors

tag: cell line_(pscs)

value: PSC4 EGFR KO B4


title: Drought5_44d_rep2


title: 9C_52700_R_epi

value: PSC4 ROSA (egfr)


title: Drought4_59d_rep2


title: soleus, Female, TH, Chow, Age 20 Week, Replicate 3


title: fat, Female, TH, Chow, Age 20 Week, Replicate 2


title: 15C_52703_KO_epi


title: soleus, Female, TH, Chow, Age 20 Week, Replicate 1


title: 6C_52697_R_epi


title: Drought3_59d_rep3


title: liver, Female, TH, Chow, Age 20 Week, Replicate 1

source_name: liver


title: 8C_52706_R_epi


title: Drought3_59d_rep2


title: fat, Female, TH, Chow, Age 20 Week, Replicate 1


title: 13B_53194_N_epi


title: liver, Female, TH, Chow, Age 20 Week, Replicate 2


title: 10C_52698_R_epi


title: Drought3_59d_rep1


title: 12C_52704_KO_epi


title: 1A_53175_V_caf


title: 11C_52707_KO_epi


title: 18_T69A + PSC4 KO A3_Fibro

source_name: Fibro

growth_protocol: PSCs and pancreatic tumor organoids were co-cultured in Matrigel for 3.5 days in reduced/control media

extract_protocol: Samples were collected in 1 mL of TRIzol Reagent and stored at -80C. The RNA was extracted using the the PureLink RNA mini kit (12183018A; Invitrogen)

value: Fibro

value: KO


title: 2_T69A + PSC4 Rosa_Tum

source_name: Organoid

value: Organoid

value: WT


title: Well-watered2_59d_rep3


title: 15_T6-LOH + PSC5 KO C5_Tum


title: Pancreas, Female, B6, HF, Age 5 Week, Replicate 7

source_name: Pancreas

value: Pancreas

value: HF


title: Pancreas, Female, B6, HF, Age 5 Week, Replicate 5


title: Pancreas, Female, B6, HF, Age 5 Week, Replicate 6


title: 14C_52701_KO_epi


title: 8_T6-LOH + PSC4 KO B4_Tum


title: Well-watered2_59d_rep1


title: 7C_52699_R_epi


title: Pancreas, Female, B6, HF, Age 5 Week, Replicate 4


title: 24_T12-LOH + PSC4 KO A3_Fibro


title: 6_T6-LOH + PSC4 Rosa_Tum


title: soleus, Female, B6, HF, Age 5 Week, Replicate 6

value: soleus


title: 28_T6-LOH + PSC5 KO D4_Fibro


title: 17_T69A + PSC4 Rosa_Fibro


title: liver, Female, B6, HF, Age 5 Week, Replicate 6


title: Well-watered2_59d_rep2

value: Nipponbare


title: 12_T12-LOH + PSC4 KO B4_Tum


title: 27_T6-LOH + PSC5 KO C5_Fibro


title: 19_T69A + PSC4 KO B4_Fibro


title: Drought4_56d_rep1


title: 23_T12-LOH + PSC4 Rosa_Fibro


title: soleus, Female, B6, HF, Age 5 Week, Replicate 5


title: 16_T6-LOH + PSC5 KO D4_Tum


title: fat, Female, B6, HF, Age 5 Week, Replicate 6


title: 11_T12-LOH + PSC4 KO A3_Tum


title: 7_T6-LOH + PSC4 KO A3_Tum


title: Drought3_56d_rep1


title: Drought3_56d_rep2


title: Drought3_56d_rep3


title: Drought4_56d_rep3


title: fat, Female, B6, HF, Age 5 Week, Replicate 5


title: 10_T12-LOH + PSC4 Rosa_Tum


title: 22_T6-LOH + PSC4 KO B4_Fibro


title: 21_T6-LOH + PSC4 KO A3_Fibro


title: Well-watered2_56d_rep3


title: Drought4_56d_rep2


title: 25_T12-LOH + PSC4 KO B4_Fibro


title: soleus, Female, B6, HF, Age 5 Week, Replicate 4


title: 26_T6-LOH + PSC5 Rosa_Fibro


title: Well-watered2_56d_rep2


title: liver, Female, B6, HF, Age 5 Week, Replicate 5

value: liver


title: 3D_54200+54201_CD90+

source_name: CAFs from PDAC tumors

extract_protocol:
Samples were collected in 1 mL of TRIzol Reagent and stored at -80C. The RNA was extracted using the RNeasy Micro kit (74004; Qiagen)
mRNA library preparation was performed using the SMART-Seq® Stranded Kit (634442, Takara Bio)
We used 7mL per samples with a total RNA yield between 0.1ng and 1.2ng (RNA integrity number between 3.1 and 8.7). For the PCR steps, we performed 10 cDNA PCR cycles for samples <0.5ng and
5 cDNA PCR cycles for samples >0.6ng.For the final PCR step, we performed 14 PCR cycles. Samples with a total RNA yield <0.5ng were eluted in 12mL, while samples with a total RNA yield >0.5ng were eluted in 18mL. The samples were run on 1 lane of MiSeq V2 nano to check for the balance.

value: CAFs from PDAC tumors


title: 4_T69A + PSC4 KO B4_Tum


title: 14_T6-LOH + PSC5 Rosa_Tum


title: liver, Female, B6, HF, Age 5 Week, Replicate 4

value: F


title: 20_T6-LOH + PSC4 Rosa_Fibro


title: Well-watered2_56d_rep1


title: 8D_54200+54201_CD90-


title: Drought2_56d_rep2


title: soleus, Female, B6, HF, Age 5 Week, Replicate 3


title: 4D_54206+208+210_CD90+


title: liver, Female, B6, HF, Age 5 Week, Replicate 3


title: Drought2_56d_rep1


title: fat, Female, B6, HF, Age 5 Week, Replicate 3


title: Drought4_59d_rep1


title: 6D_54191+92+94+205_CD90-


title: Drought2_56d_rep3


title: 1D_54191+92+94+205_CD90+


title: liver, Female, B6, HF, Age 5 Week, Replicate 2


title: 9D_54206+208+210_CD90-


title: 7D_54198_CD90-


title: fat, Female, B6, HF, Age 5 Week, Replicate 4


title: Drought1_56d_rep3


title: 10D_54207_CD90-


title: M3-SetDB1

city: Shanghai

first: JIng

last: Xue

address: No.1630 dongfang road, pudong new district, Shanghai

institute: Renji Hospital, School of Medicine,Shanghai Jiaotong University

data_processing:
Sequenced reads were trimmed for adaptor sequence and to discard reads shorter than 50bp, then mapped to mm10 whole genome using Bowtie2 v. 2.4.2
Reads Per Kilobase of exon per Megabase of library size were calculated using homer annotatePeaks.pl
Peaks were called using MACS2 version 2.2.7.1 with the parameters -B  -t  --broad -g mm --broad-cutoff 0.1
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Briefly, tumor cell were generated and collected .CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme).
DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme)

value: pancreatic tumor cell

value: Med21 knockout


title: 2D_54198_CD90+


title: 5D_54207_CD90+


title: M3-Med12

value: Med20 knockout


title: soleus, Female, B6, HF, Age 5 Week, Replicate 2

data_processing:
Reads were trimmed using Trimmomatic version 0.39 in PE mode, to remove Illumina adapters, to remove the first 12 bases from the reads, to crop to a maximum of 37 bases in length, to remove low quality reads, and to filter any reads less than 25 bases in length. Parameters: ILLUMINACLIP TruSeq3-PE-2.fa:2:30:10 HEADCROP:12 CROP:37 SLIDINGWINDOW:4:15 MINLEN:25
Reads were aligned to the mouse genomeGRCm39 using HISAT2 version 2.2.1 with default parameters
Alignment files were sorted by name using samtools sort -n with samtools version
Mate coordinate and insert size fields were added to alignment files with samtools fixmate using samtools version
Alignment files were sorted by position using samtools sort with samtools version
Duplicate reads were removed using samtools markdup -r with samtools version
Gene level counts were generated using the makeTxDbFromGFF and exonsBy functions from the Bioconductor package GenomicFeatures, version and the summarizeOverlaps function from the Bioconductor package GenomicAlignments, version. The latter was run with parameters mode="IntersectionStrict", singleEnd=F, ignore.strand=T, fragments=F
Gene counts were normalized using the DESeq function, and FPKM values computed using the fpkm function from Bioconductor package DESeq2 version
Assembly: Genome GRCm39 Mus_musculus.GRCm39.dna.toplevel.fa from Ensembl. Gene annotations used in creating read counts are Ensembl Genes version 108, Mus_musculus.GRCm39.108.gtf
Supplementary files format and content: raw_counts.csv is a comma deliminted file containing the raw read counts from each sample
Supplementary files format and content: normalized_counts.csv is a comma delimited file containing the normalized counts (using the DESeq function from Bioconductor package DESeq2) from each sample
Supplementary files format and content: fpkm.csv is a comma delimited file containing the FPKM values (computed using the fpkm function from Bioconductor package DESeq2) for each sample


title: Drought1_56d_rep1

data_processing:
Reads were mapped to the IRGSP-1.0 genome assembly and MSU7 gene models using the STAR aligner (Dobin et al., 2013)
Read counts were quantified using the featureCounts (Liao et al., 2014) with option” -S 2 -p -B -C -T”.
Supplementary files format and content: Tab-delimited text files include row counts for each Sample


title: fat, Female, B6, HF, Age 5 Week, Replicate 2

value: fat


title: M3-K27me3

value: Med18 knockout


title: M3-K27Ac

value: Med17 knockout


title: Well-watered1_56d_rep3


title: M2-SetDB1

value: Med16 knockout


title: M3-K9me3

value: Med19 knockout


title: liver, Female, B6, HF, Age 5 Week, Replicate 1


title: soleus, Female, B6, HF, Age 5 Week, Replicate 1


title: Well-watered1_56d_rep1


title: fat, Female, B6, HF, Age 5 Week, Replicate 1


title: M2-K27Ac

value: Med12 knockout


title: M2-K27me3

value: Med13 knockout


title: Drought4_53d_rewater2_rep3


title: L1-SetDB1

value: WT


title: M2-Med12

value: Med15 knockout


title: Pancreas, Female, B6, HF, Age 5 Week, Replicate 3

value: Pancreas

value: HF


title: Drought4_53d_rewater2_rep2

value: Nipponbare


title: L1-K27me3


title: L1-K9me3


title: L1-K27Ac


title: Pancreas, Female, B6, HF, Age 5 Week, Replicate 2


title: Drought4_53d_rewater2_rep1


title: M2-K9me3

value: Med14 knockout


title: Pancreas, Female, B6, HF, Age 5 Week, Replicate 1

value: F


title: Drought3_53d_rewater2_rep3


title: L3EFL020411--KPC1199_Med12_sg2

description:
KPC1199_gene.TPM.matrix.annot.xls
KPC1199_gene.count.matrix.annot.xls

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to mm39 with orientation mode using HISAT2  software
The mapped reads of each sample were assembled by StringTie  in a reference-based approach
differential expression analysis was performed using the DESeq2
Assembly: GRCm39
Supplementary files format and content: KPC1199_gene.TPM.matrix.annot.xls
Supplementary files format and content: KPC1199_gene.count.matrix.annot.xls

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA)

value: pancreatic tumor cell


title: Well-watered1_56d_rep2


title: soleus, Female, B6, HF, Age 20 Week, Replicate 6

value: soleus


title: L3EFL020410--KPC1199_lacz_1


title: L2EFL020412--KPC1199_Med12_sg3


title: Drought3_53d_rewater2_rep2


title: L3EFL020412--KCP1199_Med12_sg3


title: L2EFL020411--KPC1199_Med12_sg2


title: L1-Med12


title: liver, Female, B6, HF, Age 20 Week, Replicate 6

value: liver


title: L2EFL020410--KPC1199_lacz_1


title: Drought3_53d_rewater2_rep1


title: Well-watered2_53d_rewater2_rep3


title: fat, Female, B6, HF, Age 20 Week, Replicate 6

value: fat


title: L1EFL020412--KPC1199_Med12_sg3


title: Well-watered2_53d_rewater2_rep2


title: soleus, Female, B6, HF, Age 20 Week, Replicate 5


title: L1EFL020411--KPC1199_Med12_sg2


title: M3-1

data_processing:
Raw FASTQ reads were trimmed adapters generated by Trim Galore (v. 0.6.6)
then aligned to the mm10 reference genome through Bowtie2 (v.2.4.2) with the parameters --very-sensitive -X 2000. then aligned to the mm10 reference genome through Bowtie2 (v.2.4.2) with the parameters --very-sensitive -X 2000.
ATAC-seq accessible regions were called using MACS2 v 2.2.7.1 with the following parameters: --nomodel --shift -100 --extsize 200 -format BAMPE -p 0.01.
we used bedtools(v2.29.2) to remove batch effects
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Briefly, tumor cell were generated and collected. The ATAC-seq was performed according to the TruePrep Tagment Enzyme for ATACseq kit (TD501, Vazyme).
DNA libraries were constructed following the manufacturer’s instructions of the Trueprep index kit v2 (TD202, Vazyme) .


title: liver, Female, B6, HF, Age 20 Week, Replicate 5


title: Well-watered2_53d_rewater2_rep1


title: L1EFL020410--KPC1199_lacz_1


title: fat, Female, B6, HF, Age 20 Week, Replicate 5


title: M2-2


title: M2-1


title: L1-2


title: Drought4_53d_rewater1_rep2


title: Drought4_53d_rewater1_rep3


title: L1-1


title: liver, Female, B6, HF, Age 20 Week, Replicate 4


title: fat, Female, B6, HF, Age 20 Week, Replicate 4


title: MC3T3-E1 cells, IFN, Day21, rep2

city: beijing

first: lei

last: zhang

address: xueyuan road 38th

department: heath science center

institute: peking university

data_processing:
Alignment was performed with Hisat2
bam files were sorted with samtools
gene reads were censused with FeatureCounts
Assembly: mm10
Supplementary files format and content: comma-delimited csv file includes raw counts for each sample

growth_protocol: MC3T3-E1 preosteoblasts were maintained in alpha-MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Dynabeads mRNA purification kit (Invitrogen). A minimum of 3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepaied with a fragmentation buffer (Ambion).

treatment_protocol: Bone differentiation was induced by treatment of 2-day post-confluent cells (designated day 0, D0), and IFN groups were treated with 50mg/L since differentiation.

value: preosteoblasts

value: bone differentiation, IFN


title: MC3T3-E1 cells, IFN, Day21, rep1


title: Drought4_53d_rewater1_rep1


title: MC3T3-E1 cells, IFN, Day14, rep1


title: soleus, Female, B6, HF, Age 20 Week, Replicate 4


title: MC3T3-E1 cells, IFN, Day14, rep2


title: MC3T3-E1 cells, IFN, Day0, rep2


title: Drought3_53d_rewater1_rep3


title: MC3T3-E1 cells, IFN, Day0, rep1


title: M3-2


title: Drought3_53d_rewater1_rep1


title: fat, Female, B6, HF, Age 20 Week, Replicate 3


title: MC3T3-E1 cells, Control, Day21, rep2

value: bone differentiation


title: MC3T3-E1 cells, Control, Day21, rep1


title: MC3T3-E1 cells, Control, Day14, rep2


title: soleus, Female, B6, HF, Age 20 Week, Replicate 3


title: Drought1_56d_rep2


title: Well-watered2_53d_rewater1_rep3


title: Drought3_53d_rewater1_rep2


title: liver, Female, B6, HF, Age 20 Week, Replicate 2


title: MC3T3-E1 cells, Control, Day0, rep1


title: Well-watered2_53d_rewater1_rep2


title: MC3T3-E1 cells, Control, Day0, rep2


title: M25_S2

city: La Jolla

first: Simon

last: Brunel

state: California

address: 9420 Athena Cir

institute: LJI

data_processing:
Reads passing Illumina filters were filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.6.0 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Assembly: mm10
Supplementary files format and content: read count matrix with rows as genes and columns as cells

source_name: Spleen

extract_protocol:
Viable tetramer positive M25 and M09 CD4 T cells were sorted from pooled spleens of infected mice based on expression levels of CD43 and CD27. Three pools of 5 mice were used. Total RNA was purified using a miRNA easy micro kit (Qiagen) and quantified then 50-1000 pg was amplified by the Smart-seq2 protocol and cDNA was purified using AMPure XP beads (1:1 ratio; Beckman Coulter).
From this step, 1 ng cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit; Illumina). Samples were sequenced using a HiSeq2500 (Illumina) to obtain 50-bp single-end reads (TruSeq Rapid Kit; Illumina) generating in average of ~9 million mapped reads per sample.

value: Spleen

value: CD4 T cells

value: MCMV infection


title: Well-watered2_53d_rewater1_rep1


title: fat, Female, B6, HF, Age 20 Week, Replicate 2


title: M25_S1

description: AnGu_Spleen_Post_sort_CD27NEG_CD43POS__m25_D707D504

value: WT


title: M09_S5


title: soleus, Female, B6, HF, Age 20 Week, Replicate 2


title: M09_S4


title: liver, Female, B6, HF, Age 20 Week, Replicate 3


title: Drought4_53d_rep3


title: M09_S2


title: liver, Female, B6, HF, Age 20 Week, Replicate 1


title: M09_S3


title: MC3T3-E1 cells, Control, Day14, rep1


title: M09_S1

description: AnGu_Spleen_Post_sort_CD27NEG_CD43NEG__m09_D707D507


title: colon mucosa from recipient of old FMT donor_Sample R40

city: Boston

first: Samuel

last: Beck

state: MA

address: 609 Albany st.

department: Dermatology

institute: Boston University School of Medicine

data_processing:
Base calling and demultiplex was then performed on an Illumina DRAGEN server using bclconversion.
Raw RNA-seq reads (FASTQ) were aligned to the mouse genome (mm10, Genome Reference Consortium Mouse Build 38) using STAR 2.7.10a with '--quantMode GeneCounts' option to obtain the reads per gene value for each sample.
The read count data from each sample were normalized, and statistical tests were performed to determine differentially expressed genes (adjusted P value using Benjamini-Hochberg method, <0.05) using DESeq2 1.34.0.
Assembly: mm10
Supplementary files format and content: tab determined text file includes waw counts for each sample

source_name: colon mucosa

growth_protocol: A/J mice are were maintained on chow diet (adlib)

extract_protocol:
Total RNA was isolated colon mucosal scraping using Trizol (Thermo Fisher) and then quantified and quality checked using a Fragment Analyzer (Agilent, Santa Clara, CA).
One hundred and twenty-five ng of RNA was then used as input for library preparation using a stranded mRNA Library preparation kit following manufacturer instructions (Illumina, San Diego, CA).

treatment_protocol: Mice received antibiotics to deplete resident microbes then received 3 fecal microbiota transplants from young (R1-R20) or old (R21 -R40) donor mice. Mice were then subjected to 6 weekly injectors of azoxymethane (5-10 mg/kg). Mice were maintained for 19 weeks after final azoxymethane injection during which time they received monthly FMT boosters from the respective donor.

value: colon mucosa

value: Female

tag: donor age

value: Old

value: A/J wildtype

value: FMT from old donor


title: Pancreas, Female, B6, HF, Age 20 Week, Replicate 7

value: Pancreas

value: F

value: HF


title: Drought3_53d_rep3

value: Nipponbare


title: Drought4_53d_rep1


title: Drought4_53d_rep2


title: colon mucosa from recipient of old FMT donor_Sample R38


title: colon mucosa from recipient of old FMT donor_Sample R37


title: Pancreas, Female, B6, HF, Age 20 Week, Replicate 6


title: Drought3_53d_rep2


title: colon mucosa from recipient of old FMT donor_Sample R35


title: fat, Female, B6, HF, Age 20 Week, Replicate 1

value: fat


title: soleus, Female, B6, HF, Age 20 Week, Replicate 1

value: soleus


title: colon mucosa from recipient of old FMT donor_Sample R32


title: colon mucosa from recipient of old FMT donor_Sample R34


title: Drought3_53d_rep1


title: colon mucosa from recipient of old FMT donor_Sample R31


title: Pancreas, Female, B6, HF, Age 20 Week, Replicate 5


title: colon mucosa from recipient of old FMT donor_Sample R30

value: Male


title: Well-watered2_53d_rep3


title: colon mucosa from recipient of old FMT donor_Sample R29


title: colon mucosa from recipient of old FMT donor_Sample R28


title: Pancreas, Female, B6, HF, Age 20 Week, Replicate 3


title: colon mucosa from recipient of old FMT donor_Sample R27


title: colon mucosa from recipient of old FMT donor_Sample R39


title: colon mucosa from recipient of old FMT donor_Sample R26


title: colon mucosa from recipient of old FMT donor_Sample R25


title: Well-watered2_53d_rep1


title: Well-watered2_53d_rep2


title: colon mucosa from recipient of old FMT donor_Sample R24


title: Pancreas, Female, B6, HF, Age 20 Week, Replicate 2


title: colon mucosa from recipient of old FMT donor_Sample R23


title: Pancreas, Female, B6, HF, Age 20 Week, Replicate 1


title: colon mucosa from recipient of young FMT donor_Sample R20

value: Young

value: FMT from young donor


title: Pancreas, Female, B6, Chow, Age 5 Week, Replicate 6

value: Chow


title: colon mucosa from recipient of young FMT donor_Sample R19


title: colon mucosa from recipient of old FMT donor_Sample R21


title: Drought2_53d_rep3


title: Pancreas, Female, B6, Chow, Age 5 Week, Replicate 5


title: Drought2_53d_rep2


title: colon mucosa from recipient of young FMT donor_Sample R18


title: colon mucosa from recipient of young FMT donor_Sample R17


title: Drought1_53d_rep3


title: Pancreas, Female, B6, HF, Age 20 Week, Replicate 4


title: colon mucosa from recipient of young FMT donor_Sample R16


title: Pancreas, Female, B6, Chow, Age 5 Week, Replicate 4


title: Drought2_53d_rep1


title: colon mucosa from recipient of young FMT donor_Sample R14


title: Pancreas, Female, B6, Chow, Age 5 Week, Replicate 3


title: Drought1_53d_rep2


title: colon mucosa from recipient of young FMT donor_Sample R13


title: Drought1_53d_rep1


title: colon mucosa from recipient of young FMT donor_Sample R11


title: Pancreas, Female, B6, Chow, Age 5 Week, Replicate 2


title: colon mucosa from recipient of young FMT donor_Sample R9


title: Well-watered1_53d_rep3


title: colon mucosa from recipient of young FMT donor_Sample R8


title: Pancreas, Female, B6, Chow, Age 5 Week, Replicate 1


title: colon mucosa from recipient of young FMT donor_Sample R6


title: colon mucosa from recipient of young FMT donor_Sample R5


title: soleus, Female, B6, Chow, Age 5 Week, Replicate 6


title: colon mucosa from recipient of young FMT donor_Sample R7


title: Well-watered1_53d_rep1


title: colon mucosa from recipient of young FMT donor_Sample R4


title: colon mucosa from recipient of young FMT donor_Sample R3


title: colon mucosa from recipient of young FMT donor_Sample R15


title: Drought4_50d_rep2


title: soleus, Female, B6, Chow, Age 5 Week, Replicate 5


title: colon mucosa from recipient of young FMT donor_Sample R2


title: colon mucosa from recipient of young FMT donor_sample R1


title: fat, Female, B6, Chow, Age 5 Week, Replicate 6


title: Tfamflox/flox Cre-lyz2 +TS rep 1

city: Chengdu

first: tianqi

last: lu

address: qinglong

institute: The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: The reads were mapped to Mus_musculus.GRCm38.dna.toplevel.fa and annotated with Mus_musculus.GRCm38.98.gtf.
Supplementary files format and content: tab-delimited text files include readcount values for each Sample ...

source_name: bone marrow

growth_protocol: The bone marrow cells from mice were pooled, filtered through a 70 μm nylon mesh filter (Corning, USA), centrifuged and resuspended in ACK lysis buffer for 5 min of incubation on ice. After rinsing by medium, the bone marrow cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS (Gibco, USA), 100 U/mL penicillin/streptomycin (Gibco, USA) and additions of 1 mM sodium pyruvate, 50 µM β-mercaptoethanol (β-ME), 20 ng/mL GM-CSF and 15 ng/mL IL-4 for BMDCs differentiation. The non-adherent and loosely adherent cells were collected as BMDCs.

extract_protocol:
Total RNA was isolated from BMDCs (treated with or without TS ) of Tfam-/- and control mice using the TRIzol reagent kit.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit by the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and samples with RIN scores above 6 and a minimum total RNA of 100 ng were used for further library construction. PCR products were purified using the AMPure XP system, and library quality was assessed using the Agilent Bioanalyzer 2100 system.

treatment_protocol: The tumor supernatant of LLC cells was harvested, filtrated by 0.22 μm filters, and added to the BMDCs at a final dilution of 1:3 for 24 h of incubation.

value: bone marrow

value: bone marrow-derived dendritic cells

value: Tfamflox/flox Cre-lyz2

value: treated with LLC  tumor supernatant (TS)


title: Tfamflox/flox Cre-lyz2 +TS rep 2


title: Drought4_50d_rep1


title: Control BMDCs +TS rep 2

value: WT


title: Drought3_50d_rep3


title: Tfamflox/flox Cre-lyz2 rep 3

value: without LLC  tumor supernatant (TS)


title: liver, Female, B6, Chow, Age 5 Week, Replicate 5

first: James

last: Denvir

address: One John Marshall Drive

institute: Marshall University School of Medicine

value: liver


title: Well-watered1_53d_rep2

first: FUMIYUKI

last: SOMA

address: 2-1-2 Kan-non-dai

institute: National Agriculture and Food Research Organization


title: fat, Female, B6, Chow, Age 5 Week, Replicate 5


title: Tfamflox/flox Cre-lyz2 rep 2


title: Drought3_50d_rep2


title: colon mucosa from recipient of young FMT donor_Sample R12

value: colon mucosa

value: Female

value: A/J wildtype


title: Tfamflox/flox Cre-lyz2 rep 1


title: soleus, Female, B6, Chow, Age 5 Week, Replicate 4

value: F


title: Drought4_50d_rep3

value: Nipponbare


title: liver, Female, B6, Chow, Age 5 Week, Replicate 6


title: Control BMDCs rep 3


title: Control BMDCs rep 2


title: fat, Female, B6, Chow, Age 5 Week, Replicate 4

value: fat


title: Well-watered2_50d_rep3


title: Drought3_50d_rep1


title: liver, Female, B6, Chow, Age 5 Week, Replicate 4


title: Control BMDCs rep 1


title: Kidney, Pkd1 KO + salsalate, replicate 12

city: Leiden

first: Anish

last: Kanhai

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.
Sequencing files were then processed using the opensource BIOWDL RNAseq pipeline v4.1.0 (https://zenodo.org/record/3975552) developed at the LUMC. This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), RNAseq read alignment, read quantification, and optionally transcript assembly
FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with default settings
RNAseq reads’ alignment was performed using STAR (v2.7.5a) on GRCm39 mouse reference genome (Ensembl v103). The gene read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=yes”
Assembly: GRCm39
Supplementary files format and content: Tab-separated values file, containing raw counts for each sample

source_name: Kidney

growth_protocol: iKspCre-Pkd1del mice have a homozygously bred kidney–specific, tamoxifen–inducible Cre and two LoxP sites that flank exons 2–11 of the Pkd1 gene. The mice received tamoxifen (150 mg/kg) by oral gavage on days PN18 and PN19 to induce adult onset PKD. At PN30 the PKD mutant mice started on normal chow and randomly allocated to different groups. At PN81, the PKD mutant mice were split in two groups; 1 group continued on the normal chow and the second group were switched to the chow supplemented with 2.5 g/kg salsalate. Blood Urea (BU) levels were monitored weekly and the mice with end stage renal disease (ESRD, BU >20 mmol/L) were sacrificed. The experiment continued until PN95, when all mice were sacrificed. The kidneys from mice not receiving tamoxifen were used as wildtype controls.

extract_protocol:
The total RNA was extracted with Trizol reagent following standard protocols, after which samples were DNase treated to minimize genomic DNA contamination. The integrity of the RNA sample was assessed using the Fragment Analyzer (Agilent Technologies) to ensure that the RNA integrity number (RIN) was sufficient for library preparation
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: All kidney samples were snapped frozen in liquid nitrogen, and stored in a -80°C freezer.

value: Male

value: Kidney

value: Pkd1 KO

value: Salsalate, 2 weeks

value: 95 days


title: Kidney, Pkd1 KO + salsalate, replicate 10


title: soleus, Female, B6, Chow, Age 5 Week, Replicate 3

city: Huntington

value: soleus

value: Chow


title: Well-watered2_50d_rep2

city: Tsukuba


title: Control BMDCs +TS rep 1

value: bone marrow

value: bone marrow-derived dendritic cells

value: treated with LLC  tumor supernatant (TS)


title: Kidney, Pkd1 KO + salsalate, replicate 9


title: liver, Female, B6, Chow, Age 5 Week, Replicate 3

value: liver


title: Kidney, Pkd1 KO + salsalate, replicate 8


title: Drought2_50d_rep3


title: fat, Female, B6, Chow, Age 5 Week, Replicate 3


title: soleus, Female, B6, Chow, Age 5 Week, Replicate 2


title: Drought2_50d_rep2


title: Kidney, Pkd1 KO + salsalate, replicate 5


title: Kidney, Pkd1 KO + salsalate, replicate 6


title: Drought2_50d_rep1


title: Kidney, Pkd1 KO + salsalate, replicate 7


title: Kidney, Pkd1 KO + salsalate, replicate 3


title: liver, Female, B6, Chow, Age 5 Week, Replicate 2


title: Kidney, Pkd1 KO + salsalate, replicate 2


title: Drought1_50d_rep3


title: Kidney, Pkd1 KO + salsalate, replicate 4


title: Kidney, Pkd1 KO, replicate 12

value: Untreated


title: Well-watered2_50d_rep1


title: Kidney, Pkd1 KO + salsalate, replicate 11


title: Drought1_50d_rep2


title: fat, Female, B6, Chow, Age 5 Week, Replicate 2


title: Kidney, Pkd1 KO, replicate 10


title: Well-watered1_50d_rep3


title: Kidney, Pkd1 KO, replicate 9


title: Kidney, Pkd1 KO, replicate 8


title: Kidney, Pkd1 KO, replicate 7


title: liver, Female, B6, Chow, Age 5 Week, Replicate 1


title: Drought1_50d_rep1


title: Kidney, Pkd1 KO, replicate 6


title: Well-watered1_50d_rep2


title: Kidney, Pkd1 KO, replicate 5


title: Pancreas, Female, B6, Chow, Age 20 Week, Replicate 9

value: Pancreas


title: Kidney, Pkd1 KO + salsalate, replicate 1


title: Kidney, Pkd1 KO, replicate 4


title: soleus, Female, B6, Chow, Age 5 Week, Replicate 1


title: Kidney, Pkd1 KO, replicate 3


title: Kidney, Pkd1 KO, replicate 11


title: Pancreas, Female, B6, Chow, Age 20 Week, Replicate 8


title: Kidney, Pkd1 KO, replicate 1


title: Drought4_47d_rep3


title: Kidney, wildtype, replicate 8

value: Wildtype

value: 109 days


title: Pancreas, Female, B6, Chow, Age 20 Week, Replicate 7

value: F


title: Drought4_47d_rep2

value: Nipponbare


title: Pancreas, Female, B6, Chow, Age 20 Week, Replicate 6


title: Kidney, wildtype, replicate 5

value: Male


title: Kidney, wildtype, replicate 6

value: Kidney


title: Kidney, wildtype, replicate 4


title: soleus, Female, B6, Chow, Age 20 Week, Replicate 6


title: liver, Female, B6, Chow, Age 20 Week, Replicate 6


title: Zebrafish embryos, Strain: TPC2 mutant, Stage: 17-18 somite (Biol rep 5)

city: Hong Kong

first: Andrew

last: Miller

address: Division of LIFS, HKUST, Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
Performed adapter trimming with cutadapt v3.4 software with parameters: "--minimum-length=30 -a A\{100\} -A A\{100\} -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -g AGATGTGTATAAGAGACAG -G AGATGTGTATAAGAGACAG".
Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters "--outSAMtype BAM SortedByCoordinate --quantMode GeneCounts".
Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0.
Assembly: danRer10 (Genome Reference Consortium Zebrafish Build 10)
Supplementary files format and content: all.tsv: Tab-delimited text file includes raw counts.
Supplementary files format and content: Treatment_1-vs-Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.

organism: Danio rerio

source_name: Whole embryo

growth_protocol: Embryos were collected from wild-type ABTU and mutant TPC2 fish line and kept at 28 °C.

extract_protocol:
RNA extraction was performed using RNAzol® according to the manufacturer’s instructions.
Samples were submitted to the Bioscience Central Research Facility for library construction.

value: Whole embryo

value: TPC2 mutant

value: 17-18 somite stage


title: Drought3_47d_rep2


title: Kidney, wildtype, replicate 2


title: Well-watered1_50d_rep1


title: Kidney, Pkd1 KO, replicate 2

value: Pkd1 KO

value: 95 days


title: Zebrafish embryos, Strain: TPC2 mutant, Stage: 17-18 somite (Biol rep 4)


title: Drought3_47d_rep1


title: Kidney, wildtype, replicate 1


title: Kidney, wildtype, replicate 7


title: Zebrafish embryos, Strain: TPC2 mutant, Stage: 17-18 somite (Biol rep 3)


title: PSC5_TGFb_2

data_processing:
Estimated transcript counts were counted using Salmon (version 1.4.0)
DEA was performed in R using DESeq package (V2) with default parameters.
GSEA was performed using genes ranked by their p-values using the GSEA program (Broad Institute)
Assembly: GRCm38 (mm10)
Supplementary files format and content: Raw count data in tab-delimited text format.

source_name: PSC5 in control media with 20 ng/mL TGFbeta #2

growth_protocol: PSCs were grown in Matrigel

extract_protocol:
Samples were collected in 1 mL of TRIzol Reagent and stored at -80C. The RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).
mRNA library preparations (Illumina) were performed using 30 µL of 10 ng/mL (300 ng) per sample

treatment_protocol: PSCs were treated with the conditiones detailed above for 4 days

value: Murine pancreatic stellate cells (PSCs)

value: WT

tag: agent

value: TGFbeta

value: Day 4

tag: passage


title: Drought4_47d_rep1

growth_protocol: Rice plants were grown in a growth chamber under a 14 h light/10 h dark photoperiod, with 50% R.H. at daytime and 60% R.H. at nighttime. The temperature in the growth chamber varied from 25°C to 30℃ at daytime,

tag: tissue


title: Well-watered2_47d_rep3


title: soleus, Female, B6, Chow, Age 20 Week, Replicate 5

value: soleus

tag: Sex

tag: strain

value: Chow


title: Well-watered2_47d_rep2


title: liver, Female, B6, Chow, Age 20 Week, Replicate 5

value: liver

tag: diet

tag: age


title: Kidney, wildtype, replicate 3

tag: genotype

value: Wildtype

tag: treatment

value: Untreated

value: 109 days


title: Zebrafish embryos, Strain: TPC2 mutant, Stage: 17-18 somite (Biol rep 2)

tag: developmental stage


title: Zebrafish embryos, Strain: TPC2 mutant, Stage: 17-18 somite (Biol rep 1)


title: PSC5_TGFb_1

source_name: PSC5 in control media with 20 ng/mL TGFbeta #1

tag: cell type


title: Drought3_47d_rep3

value: Nipponbare


title: Well-watered2_47d_rep1


title: fat, Female, B6, Chow, Age 20 Week, Replicate 5

value: fat

value: F


title: fat, Female, B6, Chow, Age 20 Week, Replicate 6


title: Zebrafish embryos, Strain: ABTU, Stage: 17-18 somite (Biol rep 5)

value: Whole embryo

value: ABTU


title: Drought2_47d_rep3


title: soleus, Female, B6, Chow, Age 20 Week, Replicate 4


title: PSC5_cntrl_2

source_name: PSC5 in control media #2

tag: cell line

value: Control Media


title: Zebrafish embryos, Strain: ABTU, Stage: 17-18 somite (Biol rep 4)

value: 17-18 somite stage


title: fat, Female, B6, Chow, Age 5 Week, Replicate 1


title: Drought2_47d_rep1


title: fat, Female, B6, Chow, Age 20 Week, Replicate 4


title: PSC5_cntrl_1

source_name: PSC5 in control media #1

value: Murine pancreatic stellate cells (PSCs)


title: Zebrafish embryos, Strain: ABTU, Stage: 17-18 somite (Biol rep 2)

value: WT


title: soleus, Female, B6, Chow, Age 20 Week, Replicate 3