title: Dioscin

first: Zhiguang

last: Shi

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 v2.1.0 with default parameters
Read counts were calculated using Htseq-count with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each Sample

source_name: Dioscin

extract_protocol:
Hearts 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

treatment_protocol: Dioscin treatment for 4 weeks after TAC surgery

tag: tissue

value: Heart

value: TAC with Dioscin


title: TEC1_3IAA_C_S36_RNA-seq

status: Public on Aug 01 2023

type: SRA

city: SEATTLE

first: Lakshmi

last: Mahendrawada

state: WA

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

country: USA

institute: Fred Hutchinson Cancer Center

library_source: transcriptomic

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained from DESeq2 analysis

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 TEC1-3xV5 IAA7::URA3

growth_protocol: 30 degrees in a synthetic complete (SC) medium to mid-log phase.

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

treatment_protocol: After reaching appropriate OD samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of TFs. Newly synthesized RNA molecules were labeled for 5 minute with 4TU.For experiments conductions under specific stress conditions,  selected samples were treated with either DMSO or SM, Raffinose or Galactose, no heat shock (30°C) or heat shock (37°C)

tag: genotype

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 TEC1-3xV5 IAA7::URA3


title: MDP1_#1 cKD  Day7  biol rep 1

city: Niigata

first: Shaban

middle: Amina

last: Kaboso

address: Asahimachi-Dori 1-757l, Chuo

department: Bacteriology

country: Japan

institute: Niigata University

description: VC-MDP1_#1 cKD_day7.csv

data_processing:
Mapped forward.fastq and reverse.fastq to Mycobacterium_bovis_bcg.ASM70565v1.dna.nonchromosomal.fa with default settings using BWA
Counted the number of reads in featureCounts in pair-end mode
Calculated significant differences between gene expression with DESeq2
Assembly: Mycobacterium_bovis_bcg.ASM70565v1.dna.nonchromosomal.fa
Supplementary files format and content: CSV format calculated by DESeq2

organism: Mycobacterium tuberculosis variant bovis

source_name: BCG Tokyo 172

growth_protocol: BCG cultures were grown in 7H9/ADC containing 20 µg/ml kanamycin and 50 µg/ml hygromycin as standing cultures at 37 degrees celcius.

extract_protocol:
RNA was harvested using Direct-Zol RNA MiniPrep kit (Zymo research) following manufacturer's protocol
cDNA sample was randomly fragmented followed by 5' and 3' adapta ligation. Alternatively  "tagmentation" was done to combine the fragmentation and ligation in a single more efficient step. Adapter-ligated fragments were then PCR amplified and gel purified

treatment_protocol: For induction and maintainance of sgRNA and dcas9 expression the cultures were supplimented with Anhydrotetracycline at a final concentration of 200ng/ml every 48 hrs

tag: strain

value: BCG Tokyo 172

tag: treatment

value: Anhydrotetracycline 200ng/ml every 48 hours

value: hupB_#1 conditional knockdown

tag: time

value: Day 7


title: MDP1_#1 cKD  Day7  biol rep 2

description: VC-MDP1_#1 cKD_day7.csv


title: TEC1_DMSO_B_S32_RNA-seq


title: TEC1_3IAA_A_S34_RNA-seq


title: SWI6_DMSO_C_S50_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SWI6-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SWI6-3xV5 IAA7::URA3


title: TAC

city: Nanjing

country: China

organism: Mus musculus

source_name: TAC

value: TAC


title: VC  Day7  biol rep 3

description: VC-MDP1_#1 cKD_day7.csv

value: WT


title: MDP1_#2 cKD  Day7  biol rep 2

description: VC-MDP1_#2 cKD_day7.csv

value: hupB_#2 conditional knockdown


title: NkxDot1cKO_5_dt

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

country: Germany

institute: University of Freiburg

data_processing:
Fastq Quality Control using FastQC.
Adapter trimming and quality filtering was done using Cutadapt (Galaxy v. 4.0) with the following configurations: --paired --error-rate=0.1 --times=1 --overlap=3   --action=trim      --minimum-length=20 --pair-filter=any   --quality-cutoff=20 -a AGATCGGAAGAGC
Trimmed and quality filtered RNA-Seq reads were aligned to mm10 genome assembly using RNA STAR (Galaxy Version 2.7.8a+galaxy0) with the following configurations: outSAMtype BAM SortedByCoordinate  --twopassMode None ''  --quantMode GeneCounts   --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM ch  --outSAMprimaryFlag OneBestScore  --outSAMmapqUnique 60   --outSAMunmapped Within  --outFilterType Normal --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 1.0 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outSAMmultNmax -1 --outSAMtlen 1   --outBAMsortingThreadN  --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM
Gene level counts were obtained by running featurecounts. Featurecounts  (Galaxy Version 2.0.1+galaxy2) options:-o "output" -T   -s  0  -Q  10     -t 'exon' -g 'gene_id'    --minOverlap  1 --fracOverlap 0 --fracOverlapFeature 0    -p    -C
DESeq2 (v. 1.34.0) in R (4.2.0) on count matrices output from featurecounts. A linear model controlling for batch effects of litter and sex (∼sex +litter + genotype) was used and log2(Fold Change) shrinkage was applied. Limma remove batcheffects() was applied to VST counts.
Assembly: mm10
Supplementary files format and content: raw and normalised counts, DESEQ2 results tables

source_name: dorsal telencephalon

extract_protocol:
Ventral and dorsal telencephalon from E14.5 embryos were snap frozen in liquid nitrogen immediately after dissection and stored at -80°C. Total RNA was isolated using the RNeasy RNA isolation kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared using the TruSeq total RNA sample preparation kit from Illumina, following the manufacturer’s instructions.

value: dorsal telencephalon

tag: dissection age


title: SWI6_DMSO_B_S49_RNA-seq


title: VC  Day7  biol rep 2

description: VC-MDP1_#1 cKD_day7.csv


title: Tumor_KO_4T1OECTL_rep2

type: RNA

city: Blacksburg

first: Irving

middle: Coy

last: Allen

state: VA

address: 295 Duck Pond Dr

institute: Virginia Tech

description: Clariom S Affymetrix and ThermoFisher

hyb_protocol: Performed by ThermoFisher ClariomS services

data_processing: CHP data provided by ThermoFisher ClariomS services. Researchers analysed data using the Transcriptome Analysis Console (ThermoFisher, Applied Biosystems)

label: Biotin

source_name: 4T1 tumor (overexpression control) from Nlrx1-/- mouse

growth_protocol: 4T1 cells (4T1, 4T1OE, or 4T1OE-CTL) were injected into a singular mammary fat pad in the mouse. After the tumor had grown, tumors were collected following euthanasia and flash frozen.

extract_protocol: Qiagen Rneasy extraction kit per manufacturer's protocols

tag: mouse genotype

value: Nlrx1-/- BALB/c

tag: 4t1 cell line

value: 4T1OE-CTL (overexpression controls)


title: Tumor_KO_4T1OECTL_rep1

description: Clariom S Affymetrix and ThermoFisher

scan_protocol: Performed by ThermoFisher ClariomS services


title: SWI6_DMSO_A_S48_RNA-seq


title: VC  Day7  biol rep 1

description: VC-MDP1_#1 cKD_day7.csv


title: NkxDot1cKO_3_dt


title: SWI6_3IAA_C_S53_RNA-seq


title: MDP1_#2 cKD  Day4  biol rep 3

description: VC-MDP1_#2 cKD_day4.csv

value: Day 4


title: NkxDot1lcKO_2_dt


title: SWI6_3IAA_B_S52_RNA-seq


title: MDP1_#2 cKD  Day4  biol rep 2

description: VC-MDP1_#2 cKD_day4.csv


title: NkxDot1lcKO_1_dt


title: Tumor_KO_4T1OE_rep2

description: Clariom S Affymetrix and ThermoFisher

source_name: 4T1 tumor (overexpressing NLRX1) from Nlrx1-/- mouse

label_protocol: Performed by ThermoFisher ClariomS services

value: 4T1OE (overexpression of NLRX1)


title: MDP1_#2 cKD  Day4  biol rep 1

description: VC-MDP1_#2 cKD_day4.csv


title: WT_5_dt


title: Tumor_KO_4T1OE_rep1

description: Clariom S Affymetrix and ThermoFisher


title: MDP1_#1 cKD  Day4  biol rep 3

description: VC-MDP1_#1 cKD_day4.csv


title: Tumor_WT_4T1OECTL_rep2

description: Clariom S Affymetrix and ThermoFisher

source_name: 4T1 tumor (overexpression control) from WT mouse

value: WT BALB/c


title: SWI6_3IAA_A_S51_RNA-seq


title: Tumor_WT_4T1OE_rep2

description: Clariom S Affymetrix and ThermoFisher

source_name: 4T1 tumor (overexpressing NLRX1) from WT mouse


title: Tumor_WT_4T1OECTL_rep1

description: Clariom S Affymetrix and ThermoFisher


title: SWI5_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SWI5-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SWI5-3xV5 IAA7::URA3


title: SWI5_DMSO_B_S20_RNA-seq


title: MDP1_#1 cKD  Day4  biol rep 2

description: VC-MDP1_#1 cKD_day4.csv


title: NkxDot1cKO_4_dt


title: WT_4_dt


title: Tumor_WT_4T1OE_rep1

description: Clariom S Affymetrix and ThermoFisher


title: WT_3_dt


title: SWI5_DMSO_A_S19_RNA-seq


title: Tumor_KO_4T1_rep1

description: Clariom S Affymetrix and ThermoFisher. Recommend to exclude from analysis based on PCA results from ThermoFisher.

source_name: 4T1 tumor from Nlrx1-/- mouse

value: Parental (untransduced)


title: WT_2_dt


title: Epidermis_Znf750 cKO_3

city: Beer Sheva

first: Idan

last: Cohen

address: David Ben Gurion Blvd 1

department: Microbiology, Immunology and Genetics

country: Israel

institute: Ben-Gurion University

data_processing:
The sequences were quality trimmed and filtered using Trim Galore (v0.4.5) and cutadapt (v1.15).
Alignment of the reads to the mouse genome (GRCm38) was done using STAR (v2.5.2a).
The number of reads per gene per sample was counted using RSEM (v1.2.28).
Quality assessment (QA) of the process was carried out using FASTQC (v0.11.8) and MultiQC (v1.0.dev0).
We analyzed read counts for differential gene expression using the DESeq2 R package
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Skin epidermis

extract_protocol:
Newborn P0 back skins were collected and subjected to 1.26 U/ml Dispase for 4-6 hours at 4°C. The epidermis was isolated from the dermis and dissociated by warm 0.25% Trypsin for 10 min at 37°C. Cells were then centrifuged at 200 g for 4 min at 4°C, washed twice with 1x PBS and incubated in 350 µl Trizol for 10 min at room temp. Total RNA was purified using TriRNA Pure Kit (Geneaid) according to manufacturer’s instructions.
of total RNA per sample was used. Enrichment for poly(A) mRNA was done using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The RNA-seq libraries were then constructed following standard protocol for the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).  The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced on the Illumina NextSeq 2000 platform, obtaining 100-nucleotide single reads.

value: Skin epidermis

tag: cell line

value: Epiermal cells

tag: cell type

value: Epidermis

value: Postnatal day 0

value: Znf750 cKO


title: Tumor_KO_4T1_rep2

description: Clariom S Affymetrix and ThermoFisher


title: SWI5_3IAA_C_S24_RNA-seq


title: Tumor_WT_4T1_rep2

description: Clariom S Affymetrix and ThermoFisher

source_name: 4T1 tumor from WT mouse


title: VC  Day4  biol rep 3

description: VC-MDP1_#1 cKD_day4.csv

value: BCG Tokyo 172

value: Anhydrotetracycline 200ng/ml every 48 hours


title: MDP1_#1 cKD  Day4  biol rep 1

description: VC-MDP1_#1 cKD_day4.csv

value: hupB_#1 conditional knockdown


title: WT_1_dt

value: WT


title: SWI5_3IAA_B_S23_RNA-seq


title: Epidermis_Znf750 cKO_1


title: VC  Day4  biol rep 2

description: VC-MDP1_#1 cKD_day4.csv


title: Epidermis_Znf750 cKO_2


title: SWI5_3IAA_A_S22_RNA-seq


title: NkxDot1cKO_5_vt

source_name: ventral telencephalon

value: ventral telencephalon


title: VC  Day4  biol rep 1

description: VC-MDP1_#1 cKD_day4.csv


title: NkxDot1cKO_4_vt


title: NkxDot1cKO_3_vt


title: Epidermis_Control_3

value: Control


title: Epidermis_Control_2


title: Tumor_WT_4T1_rep1

description: Clariom S Affymetrix and ThermoFisher


title: Epidermis_Control_1


title: B. fragilis - deoxycholate 20 min - rep 2

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Reads were mapped to B. fragilis p207 genome and normalized using default settings for RNA-seq workflow in CLC Genomics Workbench v 21
Supplementary files format and content: processed data file contains total count and normalized counts (CPM) for each annotated gene in B. fragilis p207

organism: Bacteroides fragilis

source_name: bacterial cell

extract_protocol:
After treatment, culture was pelleted at 15,000 x g for 1 minute, supernatant was removed, and pellets were resuspended in 1 ml TRIzol and stored at -80°C. Samples were heated at 65°C for 10 min. Then, 200 µl chloroform was added, samples were vortexed, and incubated at room temperature for 5 min. Samples were centrifuged at 17,000 x g for 15 min at 4°C, then the upper aqueous phase was transferred to a fresh tube, an equal volume of 100% isopropanol was added, and samples were stored at -80°C overnight. Samples were centrifuged at 17,000 x g for 30 min at 4°C, the supernatant was removed, and the pellets were washed with cold 70% ethanol. Pellets were centrifuged again at 17,000 x g for 5 min at 4°C, supernatant was removed, and the pellet was allowed to dry before resuspension in 100 µl RNase-free water and incubation at 60°C for 10 min. Samples were treated with TURBO DNase and cleaned with RNeasy Mini Kit
 Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices

value: bacterial cell


title: B. fragilis - deoxycholate 20 min - rep 3


title: SWI4_DMSO_B_S14_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SWI4-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SWI4-3xV5 IAA7::URA3


title: NkxDot1lcKO_2_vt


title: NkxDot1lcKO_1_vt


title: SWI4_DMSO_A_S13_RNA-seq


title: WT_5_vt


title: Pancreas, ko_2126

city: Vancouver

first: Howard

last: Cen

state: BC

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

data_processing:
The Agilent 2100 Bioanalyzer was used to perform sample quality control.
Samples that qualified (RIN>5) were prepped using the standard protocol for Illumina Stranded mRNA prep (Illumina).
Sequencing was done using the Illumina NextSeq 2000 with paired-end 59 bp × 59 bp reads.
Sequencing data were demultiplexed using Illumina’s BCL Convert and aligned to the Mus Musculus (mm10) reference sequence using DRAGEN RNA app on Basespace Sequence Hub (https://support-docs.illumina.com/SW/DRAGEN_v41/Content/SW/DRAGEN/TPipelineIntro_fDG.htm).
De-multiplexed read sequences were then aligned to the Mus Musculous mm10 reference sequence using STAR aligner (https://www.ncbi.nlm.nih.gov/ pubmed/23104886).
Assembly was estimated using Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/) through bioinformatics apps available on Illumina Sequence Hub using default settings
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for every sample (gene symbols are rownames).

source_name: Pancreas

extract_protocol:
Total RNA were extracted with Qiagen Rneasy Kit.
Standard protocol for the NEBNext Ultra II Stranded mRNA (New England Biolabs)

value: Pancreas

tag: age

value: 12-week old

tag: Sex

value: female

value: Insr KO


title: Pancreas, ko_2124


title: SWI4_3IAA_B_S17_RNA-seq


title: B. fragilis - deoxycholate 6 min - rep 3


title: Pancreas, ko_2070


title: B. fragilis - deoxycholate 20 min - rep 1


title: WT_4_vt


title: SWI4_3IAA_A_S16_RNA-seq


title: B. fragilis - deoxycholate 6 min - rep 1


title: Pancreas, ko_2079


title: B. fragilis - deoxycholate 6 min - rep 2


title: SWI4_DMSO_C_S15_RNA-seq


title: SUT2_DMSO_C_S15_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SUT2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SUT2-3xV5 IAA7::URA3


title: Pancreas, het_2042

value: Insr Het


title: WT_3_vt


title: B. fragilis - untreated - rep 3

value: UNTREATED


title: WT_2_vt


title: WT_1_vt


title: Pancreas, het_1770


title: B. fragilis - untreated - rep 2


title: B. fragilis - untreated - rep 1


title: Pancreas, het_2066


title: SUT2_DMSO_A_S13_RNA-seq


title: UMUC3 cells 3

city: 武汉

first: Yu

last: Hua

state: State...

address: 武汉大学医学部1舍2单元

institute: 武汉大学

data_processing:
Sequencing Platform: NBSEQ-400.
Sequencing length: SE50
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
We used HISAT to align the clean reads to the reference genome.
We used Bowtie2 to align the clean reads to the reference genes.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes FPKM, TPM, read_count values for each Sample

organism: Homo sapiens

source_name: bladder cancer

growth_protocol: UMUC3 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from cells using trizol reagent (Invitrogen) and then reverse tran-scription was performed using the cDNA Reverse Transcription Kit (Toyobo Life Science, Shanghai China) to synthesize cDNA. 1 ug of total RNA was used for the construction of sequencing libraries.
In this project, we sequenced 9 samples used BGISEQ platform, averagely generating about 1.19G Gb bases per sample. The average mapping ratio with reference genome is 88.20%, the average mapping ratio with gene is 81.59%; 16886 genes were identified.

value: bladder cancer

value: Human bladder cancer cells

value: no


title: SUT2_DMSO_B_S14_RNA-seq


title: SUT2_3IAA_C_S18_RNA-seq


title: Rat CD4+ T-MBP cells, spleen Ets1 KO, rep R3

city: Planegg

first: Anneli

last: Peters

address: Großhaderner Str. 9

institute: Institute for Clinical Neuroimmunology, Biomedical Center, University Hospital of the Ludwig-Maximilians University Munich

description: Column names: R2Ets1, R1NT, R2NT, R3NT, R3Ets1, R1Ets3

data_processing:
Fastq files were aligned with RNA STAR (version 2.7.2b) to the reference genome Rnor_6.0.102 with default parameters and without trimming
HTSeq-count (version 1.0.0) was then used
Differential expression determined with DESeq2 (version 2.11.40.7+galaxy1), with estimateSizeFactors = poscounts and otherwise default parameters. Batch correction per animal was performed when applicable
All further analysis was run with R (version 4.0.0+)
Rnor_6.0
Tab-delimited txt file of DESeq2 results
Tab-delimited txt file of normalized counts output from the DESeq2 software

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Sorted CD4+ T-MBP cells from spleen

growth_protocol: Cells were transferred to Lewis rats three days before isolation. Prior to transfer, cells were kept in TCGF (complete DMEM supplemented with 10 % Horse serum and 2 % of PMA-stimulated EL4IL2 cell culture supernatant and 1 % Pen/Strep) for four days to expand the number of T cells. Then, the T cells were restimulated for two days with 50 Gy irradiated thymocytes in complete DMEM supplemented with 1 % rat serum and 10 µg/ml MBP, and transferred.

extract_protocol:
The spleen was dissected and homogenized by passing through a metal strainer. Erythrocytes were removed by treating with ACK buffer for 3 min on ice and CD4+ T cells were enriched using the EasySep™ Rat CD4+ T Cell Isolation Kit (StemCell technologies), before purification by sorting based on their fluorescent markers, BFP for control and GFP for KO
The library was prepared from total RNA using the Collibri 3' mRNA Library Prep Kits for Illumina Systems (Thermo Fisher). Amplification of transcripts was confirmed with Agilent Bioanalyzer on DNA 1000 Chips

value: Sorted CD4+ T-MBP cells from spleen

value: Ets1 KO

value: Lewis rat

value: day 3 post transfer


title: Pancreas, wt_2067

value: Insr WT


title: SWI4_3IAA_C_S18_RNA-seq


title: SUT2_3IAA_B_S17_RNA-seq


title: UMUC3 cells 2

address: 武汉大学医学部1舍2单元

value: WT


title: UMUC3 cells 1

address: 武汉大学医学部1舍2单元


title: Rat CD4+ T-MBP cells, spleen Ets1 KO, rep R2

description: Column names: R2Ets1, R1NT, R2NT, R3NT, R3Ets1, R1Ets2


title: Pancreas, wt_1860


title: Pancreas, wt_2404

extract_protocol: A piece of the tail from pancreata collected from female mice at 12 weeks of age (PK-Insrw/w (n=4), PK-Insrw/f (n=3), PK-Insrf/f (n=4)), were frozen with liquid nitrogen and shattered with a C01 Manual Pulverizer and RNA was isolated with RNeasy Micro Kit (QIAGEN, 74004).


title: SUT1_DMSO_C_S9_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SUT1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SUT1-3xV5 IAA7::URA3


title: SUT2_3IAA_A_S16_RNA-seq


title: Rat CD4+ T-MBP cells, spleen NT control to Ets1 KO, rep R3


title: UMUC3 cells, sgSTIL 5

address: 武汉大学医学部1舍2单元

value: STIL knockout

value: CRISPR-Cas9 gene editing technology


title: UMUC3 cells, sgSTIL 6

address: 武汉大学医学部1舍2单元


title: SUT1_DMSO_B_S8_RNA-seq


title: UMUC3 cells, sgSTIL 4

address: 武汉大学医学部1舍2单元


title: Rat CD4+ T-MBP cells, spleen NT control to Ets1 KO, rep R2


title: Female CCI low biol rep 2, Day3

city: Morgantown

first: Kate

last: Karelina

state: WV

address: 108 Biomedical Rd BMRC 322

department: Neuroscience

institute: West Virginia University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads were processed using Cell Ranger (version7.0.1), and FASTQ files were mapped to the GRCm38/mm10 reference genome
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
For single nuclei isolation, mice were transcardially perfused with 0.1M PBS and brains were dissected on ice. A 3mm perilesional coronal section was isolated from the ipsilateral hemisphere (AP Bregma -1 mm to -4 mm), and a block containing hippocampal and cortical tissue was then further dissected from that section (DV Bregma 0 mm to -3 mm).  The dissected tissue block was rapidly frozen and kept at -80°C before nuclear isolation.  Tissue samples were homogenized in homogenization buffer (0.32M sucrose, 5mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton-X-100, 0.1mM EDTA with PierceTM protease inhibitors). The resulting homogenate was layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2, with PierceTM protease inhibitors). Tubes were loaded into an SW 32 Ti swinging bucket and centrifuged in a Beckman Coulter Optima X Series ultracentrifuge at 25,000 rpm at 4°C for 2 hr. Nuclei were treated with a nuclease inhibitor and resuspended in 0.04% BSA in DPBS.
Isolated nuclei were processed using the 10x Genomics GEM Single Cells 3’ Kit v3.1 reagents per manufacturer’s instructions to generate barcoded single cell RNAseq libraries.  Briefly, an aliquot of each sample was diluted 1:20 with trypan blue and counted on a hemocytometer.  Based on the nuclei count, each sample was diluted to a concentration of 1200 nuclei/ml using PBS+ 0.04% BSA + 0.2 units/ml RNAse inhibitor (Millipore Sigma). The viability of the samples was 91 – 96% prior to loading the samples on a Chip G. Approximately 12,000 cells/samples were loaded on the chip with a target cell recovery of 10,000/sample, and the samples were visually observed to be opaque and uniform. Individual cell’s RNA was barcoded then stored at -20°C for < 1 week until RNAseq libraries were made.  The libraries were built using reagents provided in the 10X Genomics kit with 10X Genomics UDI’s as per manufacturer’s directions. The quality of the libraries was determined by assaying an aliquot on a high sensitivity D1000 screen tape.

value: brain

value: Swiss Webster

value: 4-6 weeks old

value: female

tag: injury

value: controlled cortical impact

tag: exercise

value: low intensity


title: SUT1_DMSO_A_S7_RNA-seq


title: UMUC3 cells, sgSTIL 3

address: 武汉大学医学部1舍2单元

value: bladder cancer

value: Human bladder cancer cells


title: Female CCI high biol rep 2, Day3

description: 10x Genomics

value: high intensity


title: Rat CD4+ T-MBP cells, parenchyma Ets1 KO, rep R3

description: Column names: R2NT, R3NT, R1NT, R3Ets1, R2Ets1, R1Ets3

source_name: Sorted CD4+ T-MBP cells from spinal cord parenchyma

extract_protocol:
The spinal cord parenchyma was dissected and homogenized by passing through a metal strainer. Lymphocytes were isolated using a 30%/64% Percoll gradient and centrifugation at 1200g, room temperature for 30min with mild acceleration and brake. Lymphocytes were collected from the interface. Cells were then FACS sorted based on fluorescent protein expression, BFP for control, GFP for KO
The library was prepared from total RNA using the Collibri 3' mRNA Library Prep Kits for Illumina Systems (Thermo Fisher). Amplification of transcripts was confirmed with Agilent Bioanalyzer on DNA 1000 Chips

value: Ets1 KO


title: Rat CD4+ T-MBP cells, spleen NT control to Ets1 KO, rep R1

description: Column names: R2Ets1, R1NT, R2NT, R3NT, R3Ets1, R1Ets1

value: Sorted CD4+ T-MBP cells from spleen

value: Lewis rat


title: SUT1_3IAA_C_S12_RNA-seq


title: SUT1_3IAA_B_S11_RNA-seq


title: UMUC3 cells, sgSTIL 2

address: 武汉大学医学部1舍2单元


title: Female sham sedentary biol rep 2, Day3

description: 10x Genomics

value: sham

value: sedentary


title: Rat CD4+ T-MBP cells, parenchyma Ets1 KO, rep R2

description: Column names: R2NT, R3NT, R1NT, R3Ets1, R2Ets1, R1Ets2

value: Sorted CD4+ T-MBP cells from spinal cord parenchyma

value: day 3 post transfer


title: UMUC3 cells, sgSTIL 1

address: 武汉大学医学部1舍2单元

value: STIL knockout

value: CRISPR-Cas9 gene editing technology


title: SUT1_3IAA_A_S10_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SUT1-3xV5 IAA7::URA3


title: Rat CD4+ T-MBP cells, spleen Ets1 KO, rep R1


title: Rat CD4+ T-MBP cells, parenchyma Ets1 KO, rep R1

description: Column names: R2NT, R3NT, R1NT, R3Ets1, R2Ets1, R1Ets1


title: Male CCI high biol rep 2, Day3

description: 10x Genomics

value: brain

value: Swiss Webster

value: 4-6 weeks old

value: male


title: Rat CD4+ T-MBP cells, parenchyma NT control, rep R3

value: WT


title: Male CCI low biol rep 2, Day3

description: 10x Genomics

value: controlled cortical impact

value: low intensity


title: Male CCI sedentary biol rep 2, Day3

description: 10x Genomics


title: SUM1_DMSO_B_S2_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SUM1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SUM1-3xV5 IAA7::URA3


title: SUM1_DMSO_C_S3_RNA-seq


title: Rat CD4+ T-MBP cells, parenchyma NT control, rep R2


title: Male sham sedentary biol rep 2, Day3

description: 10x Genomics


title: SUM1_DMSO_A_S1_RNA-seq


title: Female CCI sedentary biol rep 2, Day3

description: 10x Genomics

value: female


title: SUM1_3IAA_C_S6_RNA-seq


title: Female CCI low biol rep 1, Day3

description: 10x Genomics


title: Rat CD4+ T-MBP cells, parenchyma NT control, rep R1

value: Lewis rat


title: Spleen, week 8, 17°C, challenged fish 82

city: Ås

first: Aleksei

last: Krasnov

state: Viken

address: Øreveien, 47B

country: Norway

institute: Nofima AS

description: challenged fish 82

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Gadus morhua

source_name: Spleen

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Atlantic cod were kept in tanks with sea water

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Treatment included acclimatization to optimum and increased temperature (12°C and 17°C) and challenge with Francisella noatunensis after 8 weeks.

tag: time point

value: week 8

tag: temperature


title: Female CCI high biol rep 1, Day3

description: 10x Genomics

value: high intensity


title: SUM1_3IAA_A_S4_RNA-seq


title: Spleen, week 8, 17°C, challenged fish 79

description: challenged fish 79


title: SUM1_3IAA_B_S5_RNA-seq


title: Spleen, week 8, 17°C, challenged fish 78

description: challenged fish 78


title: Stem, 72H after MS (control, no bending), rep1 (NS72HR1)

city: Angers

first: Béra

last: LEY-NGARDIGAL

address: 2 Boulevard de Lavoisier

department: Faculté des Sciences

country: France

institute: Université d'Angers

description:
read_counts.txt
gene_fpkm.txt

data_processing:
Reads containing adapters, low-quality sequences (≤ Q20) and with more than 10% poly-N sequences were removed using a Novogene in-house workflow before de novo transcriptome assembly.
Transcriptome assembly was performed by Trinity v2.6.6 software (parameters: minKmerCov= 3,min_glue=4).
CORSET v4.6 software (parameters: -f ture, Default, -m 10) to remove redundancy from Trinity results.
BUSCO v3.0.2 (parameters: -m tran) was used to assess the quality of structural annotation of the transcriptome.
Gene expression levels were estimated for each sample using RSEM v1.2.28 software (parameters: –estimate-rspd -mismatch-rate 0.3).
Assembly: De novo sequencing
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

organism: Hydrangea macrophylla

source_name: Whole stem

growth_protocol: Micro-cuttings of Hydrangea macrophylla cv. 'Wudu'® were produced by Hortensia France (Rives-du-Loir-en-Anjou, France) for the purposes of the experiment. After approximately 5 weeks, when the root system of the micro-cuttings had completely filled the micro-plugs (Green Products, Jongkind substrate: 35% Swedish peat/27.5% brown peat/37.5% perlite; v/v/v), the plants were transferred into 10 cm diameter pots containing a mixed substrate of peat and fertilized coconut (75%/25%; v/v) fertilized by 0.70 kg Pg-Mix Haifa 12-14-25, 0.3 kg microelements, 0.70 kg limestone, 1 kg dolomite lime and 5 kg clay per m3. MS experiments were carried in a growth chamber (T° day/night: 23/21°C; RH: 80%) where plants were sub-irrigated 2 days before the start of the experiment with a nutrient solution (Angibaud-Soluveg® ALC 47; EC: 1.8 mS/cm; pH: 6). Plants were grown under a 16 h/day photoperiod from artificial light using light-emitting diodes (Topband) with a photon flux density [380-780 nm] of 100 ± 2 µmol/m²/s.

extract_protocol:
Approximately 70 mg of stems were crushed in a mortar using liquid nitrogen. RNAs were extracted using the RNA plant extraction kit (Macherey-Nagel).
RNA-Seq libraries are prepared from total RNA using poly(A) enrichment of the mRNA. Libraries of the 27 samples were sequenced using the Illumina NovaSeq 6000 PE150 (Novogene, United Kingdom).

treatment_protocol: MS device is composed of 2 arms allowing 2 simultaneous mechanical treatments, each arm moving back and forth at a speed of 12 m/h over a 2.1 m² surface area (2.1 m length x 1.0 m width). MS consisted in 12 consecutive bendings (i.e. 6 forth and 6 back) applied in the morning between 9:00 and 10:00 a.m. for a single day. The stimulation material was an unfringed 2 mm thick plastic curtain (2.3 kg/m²) with the lower part of the curtain placed 0.5 cm below the plant apex. Stems were bent by the curtain at an angle of 30° with reference to verticality for about 30 seconds.

value: Whole stem

tag: cultivar

value: Wudu

value: Control, no bending


title: Stem, 72H after MS (control, no bending), rep2 (NS72HR2)

description:
read_counts.txt
gene_fpkm.txt

tag: tissue


title: Stem, 72H after MS (control, no bending), rep3 (NS72HR3)

description:
read_counts.txt
gene_fpkm.txt

tag: genotype


title: Female sham sedentary biol rep 1, Day3

description: 10x Genomics

tag: strain

value: sham

value: sedentary


title: STP4_DMSO_B_S55_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 STP4-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STP4-3xV5 IAA7::URA3


title: Male CCI low biol rep 1, Day3

description: 10x Genomics

value: brain

value: Swiss Webster


title: Spleen, week 8, 12°C, challenged fish 67

description: challenged fish 67


title: Spleen, week 8, 12°C, challenged fish 68

description: challenged fish 68


title: STP4_DMSO_C_S56_RNA-seq


title: Male CCI high biol rep 1, Day3

description: 10x Genomics

value: 4-6 weeks old

value: male


title: Stem, 72H after MS (MS treatment), rep3 (S72HR3)

description:
read_counts.txt
gene_fpkm.txt

value: WT

tag: treatment

value: MS treatment


title: Stem, 72H after MS (MS treatment), rep1 (S72HR1)

description:
read_counts.txt
gene_fpkm.txt


title: Stem, 72H after MS (MS treatment), rep2 (S72HR2)

description:
read_counts.txt
gene_fpkm.txt


title: Spleen, week 8, 12°C, challenged fish 70

description: challenged fish 70


title: STP4_DMSO_A_S54_RNA-seq


title: Spleen, week 8, 12°C, challenged fish 66

description: challenged fish 66


title: Female CCI sedentary biol rep 1, Day3

description: 10x Genomics

value: controlled cortical impact


title: STP4_3IAA_C_S59_RNA-seq


title: Male CCI sedentary biol rep 1, Day3

description: 10x Genomics


title: Spleen, week 8, 17°C, fish 86

description: fish 86


title: Female CCI high biol rep 2, Day2

description: 10x Genomics

value: female


title: STP4_3IAA_A_S57_RNA-seq


title: Spleen, week 8, 17°C, fish 85

description: fish 85


title: Female CCI low biol rep 2, Day2

description: 10x Genomics

value: low intensity


title: Stem, 24H after MS (control, no bending), rep2 (NS24HR2)

description:
read_counts.txt
gene_fpkm.txt


title: Stem, 24H after MS (control, no bending), rep1 (NS24HR1)

description:
read_counts.txt
gene_fpkm.txt


title: Spleen, week 8, 17°C, fish 87

description: fish 87

value: week 8


title: Female CCI sedentary biol rep 2, Day2

description: 10x Genomics


title: STP2_DMSO_C_S57_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 STP2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STP2-3xV5 IAA7::URA3


title: Stem, 24H after MS (MS treatment), rep3 (S24HR3)

description:
read_counts.txt
gene_fpkm.txt

value: Whole stem


title: STP2_DMSO_B_S56_RNA-seq


title: Stem, 24H after MS (MS treatment), rep2 (S24HR2)

description:
read_counts.txt
gene_fpkm.txt

value: Wudu


title: STP2_DMSO_A_S55_RNA-seq


title: Spleen, week 8, 12°C, fish 76

description: fish 76


title: Male CCI high biol rep 2, Day2

description: 10x Genomics

value: high intensity


title: Female sham sedentary biol rep 2, Day2

description: 10x Genomics

value: sham


title: Spleen, week 8, 17°C, fish 84

description: fish 84


title: Stem, 24H after MS (control, no bending), rep3 (NS24HR3)

description:
read_counts.txt
gene_fpkm.txt

value: Control, no bending


title: STP2_3IAA_C_S60_RNA-seq


title: STP4_3IAA_B_S58_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STP4-3xV5 IAA7::URA3


title: Male CCI low biol rep 2, Day2

description: 10x Genomics

value: brain


title: Male sham sedentary biol rep1, Day3

description: 10x Genomics

value: Swiss Webster

value: sedentary


title: Stem, 3H after MS (control, no bending), rep3 (NS3HR3)

description:
read_counts.txt
gene_fpkm.txt


title: Spleen, week 8, 12°C, fish 74

description: fish 74


title: Spleen, week 8, 12°C, fish 73

description: fish 73


title: Spleen, week 1, 17°C, fish 17

description: fish 17

value: week 1


title: Stem, 24H after MS (MS treatment), rep1 (S24HR1)

description:
read_counts.txt
gene_fpkm.txt

value: WT


title: STP1_DMSO_C_S3_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 STP1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STP1-3xV5 IAA7::URA3


title: STP2_3IAA_B_S59_RNA-seq


title: Stem, 3H after MS (control, no bending), rep2 (NS3HR2)

description:
read_counts.txt
gene_fpkm.txt


title: Stem, 3H after MS (MS treatment), rep2 (S3HR2)

description:
read_counts.txt
gene_fpkm.txt

value: MS treatment


title: Male CCI sedentary biol rep 2, Day2

description: 10x Genomics

value: 4-6 weeks old

value: male

value: controlled cortical impact


title: Stem, 3H after MS (control, no bending), rep1 (NS3HR1)

description:
read_counts.txt
gene_fpkm.txt


title: STP1_DMSO_A_S1_RNA-seq


title: Spleen, week 8, 12°C, fish 75

description: fish 75

value: week 8


title: Male sham sedentary biol rep 2, Day2

description: 10x Genomics


title: Stem, 3H after MS (MS treatment), rep1 (S3HR1)

description:
read_counts.txt
gene_fpkm.txt

value: Whole stem


title: STP2_3IAA_A_S58_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STP2-3xV5 IAA7::URA3


title: Stem, 3H after MS (MS treatment), rep3 (S3HR3)

description:
read_counts.txt
gene_fpkm.txt

value: Wudu


title: Stem, 1H after MS (control, no bending), rep3 (NS1HR3)

description:
read_counts.txt
gene_fpkm.txt


title: Female CCI high biol rep 1, Day2

description: 10x Genomics

value: female

value: high intensity


title: Spleen, week 1, 12°C, fish 9

description: fish 9


title: Spleen, week 1, 17°C, fish 15

description: fish 15


title: Spleen, week 1, 12°C, fish 7

description: fish 7


title: Spleen, week 1, 17°C, fish 13

description: fish 13


title: Female CCI low biol rep 1, Day2

description: 10x Genomics

value: low intensity


title: Spleen, week 1, 17°C, fish 12

description: fish 12


title: STP1_DMSO_B_S2_RNA-seq


title: STE12_DMSO_B_S20_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 STE12-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STE12-3xV5 IAA7::URA3


title: Stem, 1H after MS (MS treatment), rep3 (S1HR3)

description:
read_counts.txt
gene_fpkm.txt


title: Stem, 1H after MS (MS treatment), rep2 (S1HR2)

description:
read_counts.txt
gene_fpkm.txt


title: Spleen, week 1, 12°C, fish 11

description: fish 11


title: Spleen, week 1, 12°C, fish 10

description: fish 10


title: Female CCI sedentary biol rep 1, Day2

description: 10x Genomics

value: brain

value: Swiss Webster


title: STE12_DMSO_A_S19_RNA-seq


title: Spleen, week 1, 17°C, fish 16

description: fish 16

value: week 1


title: STP1_3IAA_C_S6_RNA-seq


title: Female sham sedentary biol rep 1, Day2

description: 10x Genomics

value: sham

value: sedentary


title: Stem, 1H after MS (control, no bending), rep2 (NS1HR2)

description:
read_counts.txt
gene_fpkm.txt

value: WT

value: Control, no bending


title: STP1_3IAA_B_S5_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STP1-3xV5 IAA7::URA3


title: Spleen, before trial, 8°C, fish 4

description: fish 4

value: before trial


title: STE12_3IAA_C_S24_RNA-seq


title: Stem, 15min before MS (control, no bending), rep3 (T0R3)

description:
read_counts.txt
gene_fpkm.txt


title: STP1_3IAA_A_S4_RNA-seq


title: Female CCI low biol rep 2, Day1

description: 10x Genomics

value: 4-6 weeks old

value: controlled cortical impact


title: STE12_3IAA_B_S23_RNA-seq


title: Spleen, week 1, 12°C, fish 6

description: fish 6


title: Male CCI low biol rep 1, Day2

description: 10x Genomics

value: male


title: Female CCI sedentary biol rep 2, Day1

description: 10x Genomics


title: STE12_DMSO_C_S21_RNA-seq


title: Male CCI sedentary biol rep 1, Day2

description: 10x Genomics


title: Male sham sedentary biol rep1, Day2

description: 10x Genomics


title: Female sham sedentary biol rep 2, Day1

description: 10x Genomics


title: Male CCI high biol rep 1, Day2

description: 10x Genomics


title: Skin, week 8, 17°C, challenged fish 82

description: challenged fish 82

source_name: Skin

value: week 8


title: STB5_DMSO_B_S26_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 STB5-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STB5-3xV5 IAA7::URA3


title: distal_colon_day_0_replicate_4

city: Gainesville

first: Jake

last: Boles

state: FL

address: LG-152, 1149 Newell Dr

institute: University of Florida

description: colon_clean_VST_counts.csv column 63

data_processing:
Reads were filtered to remove adapters, reads with polyA or polyG, reads with more than 5% unknown nucleotides, and reads with more than 20% low-quality bases (Q-value < 20) with Cutadapt.
Reads were mapped to the GRCmm39 genome assembly using STAR (v. 2.7.9)
Reads were counted with Subread (v. 2.0.3) in paired-end mode
Quality control and normalization was performed in R with the WGCNA, DESeq2, and edgeR packages.
Assembly: GRCmm39
Supplementary files format and content: comma-separated file gives raw read counts for each sample
Supplementary files format and content: comma-separated file gives variance-stabilized counts of only high-quality genes and samples

extract_protocol:
RNA was extracted using the TRIzol-chloroform based method. Tissue was lysed in TRIzol (ThermoFisher 15596018), and lysate was mixed with phenol:choloroform:isoamyl alcohol (ThermoFisher 15593049) in a 5:1 ratio. Protein and nucleic acids were separated into phases via centrifugation. The top aqueous layer containing the RNA was passed through a QIAshredder column (Qiagen 79656). Eluent was mixed 1:1 with 70% ethanol and applied to an RNease Mini column (Qiagen 74104). After a brief centrifugation, columns were washed once with RW1 buffer and twice with RPE buffer, as per manufacturer's recommendations. RNA was eluted in nuclease-free water. 1µg of total RNA in a concentration of 20ng/µL was shipped to LC Sciences (Houston, TX) for library preparation and RNA sequencing.
Total RNA was enriched for mRNA, fragmented, and reverse transcribed into complementary DNA (cDNA). Second-stranded DNA was synthesized, A-bases were added to the blunt ends of either strand, and DNA was ligated to dual-index adapters. Size selection was performed and DNA was treated with a heat-labile UDG enzyme. Ligated products were amplified with PCR before sequencing.

treatment_protocol: Mice received 2.5% DSS in their drinking water for 7d followed by a recovery period of 14d, and tissue was harvested at the following time points: day 0, 5, 7, 9, 12, 14, 21. Mice were euthanized via rapid decapitation and tissues were flash-frozen in liquid nitrogen immediately upon removal.

tag: day

value: F


title: Female CCI high biol rep 2, Day1

description: 10x Genomics

value: female

value: high intensity


title: distal_colon_day_0_replicate_5

description: colon_clean_VST_counts.csv column 64


title: STB5_DMSO_A_S25_RNA-seq


title: Skin, week 8, 17°C, challenged fish 81

description: challenged fish 81


title: Male sham sedentary biol rep 2, Day1

description: 10x Genomics

value: brain


title: distal_colon_day_0_replicate_2

description: colon_clean_VST_counts.csv column 61


title: Spleen, before trial, 8°C, fish 2

description: fish 2


title: Spleen, before trial, 8°C, fish 1

description: fish 1


title: distal_colon_day_0_replicate_1

description: colon_clean_VST_counts.csv column 60


title: Spleen, before trial, 8°C, fish 3

description: fish 3


title: STE12_3IAA_A_S22_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STE12-3xV5 IAA7::URA3


title: Stem, 1H after MS (MS treatment), rep1 (S1HR1)

description:
read_counts.txt
gene_fpkm.txt

value: Whole stem

value: Wudu

value: MS treatment


title: Stem, 15min before MS (control, no bending), rep2 (T0R2)

description:
read_counts.txt
gene_fpkm.txt

value: WT


title: Female CCI high biol rep 1, Day1

description: 10x Genomics

value: Swiss Webster


title: Stem, 15min before MS (control, no bending), rep1 (T0R1)

description:
read_counts.txt
gene_fpkm.txt

value: Control, no bending


title: Skin, week 8, 12°C, challenged fish 68

description: challenged fish 68


title: Skin, week 8, 12°C, challenged fish 70

description: challenged fish 70


title: STB5_DMSO_C_S27_RNA-seq


title: Female CCI low biol rep 1, Day1

description: 10x Genomics

value: low intensity


title: Male CCI high biol rep 2, Day1

description: 10x Genomics

value: 4-6 weeks old


title: Male CCI low biol rep 2, Day1

description: 10x Genomics

value: controlled cortical impact


title: Skin, week 8, 17°C, challenged fish 79

description: challenged fish 79


title: Male CCI high biol rep 1, Day1

description: 10x Genomics

value: male


title: Female sham sedentary biol rep 1, Day1

description: 10x Genomics

value: sham

value: sedentary


title: distal_colon_day_0_replicate_3

description: colon_clean_VST_counts.csv column 62

value: F


title: distal_colon_day_21_replicate_3

description: colon_clean_VST_counts.csv column 56


title: Male CCI sedentary biol rep 2, Day1

description: 10x Genomics


title: distal_colon_day_21_replicate_4

description: colon_clean_VST_counts.csv column 57


title: distal_colon_day_21_replicate_2

description: colon_clean_VST_counts.csv column 55


title: Male CCI low biol rep 1, Day1

description: 10x Genomics


title: Skin, week 8, 17°C, challenged fish 78

description: challenged fish 78

value: week 8


title: distal_colon_day_9_replicate_10

description: colon_clean_VST_counts.csv column 58

value: M


title: Skin, week 8, 17°C, fish 87

description: fish 87


title: STB5_3IAA_C_S30_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STB5-3xV5 IAA7::URA3


title: distal_colon_day_21_replicate_1

description: colon_clean_VST_counts.csv column 54


title: STB5_3IAA_B_S29_RNA-seq


title: distal_colon_day_21_replicate_8

description: colon_clean_VST_counts.csv column 59


title: Male CCI sedentary biol rep 1, Day1

description: 10x Genomics

value: brain


title: Skin, week 8, 17°C, fish 85

description: fish 85


title: Skin, week 8, 17°C, fish 84

description: fish 84


title: STB1_DMSO_B_S32_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 STB1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 STB1-3xV5 IAA7::URA3


title: distal_colon_day_21_replicate_6

description: colon_clean_VST_counts.csv column 52


title: Skin, week 8, 12°C, challenged fish 66

description: challenged fish 66


title: Skin, week 8, 12°C, challenged fish 67

description: challenged fish 67


title: STB1_DMSO_A_S31_RNA-seq


title: STB5_3IAA_A_S28_RNA-seq


title: SRL3_DMSO_B_S20_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SRL3-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SRL3-3xV5 IAA7::URA3


title: Skin, week 8, 17°C, fish 86

description: fish 86


title: STB1_3IAA_C_S36_RNA-seq


title: SRL3_3IAA_C_S24_RNA-seq


title: STB1_DMSO_C_S33_RNA-seq


title: STB1_3IAA_B_S35_RNA-seq


title: Female CCI sedentary biol rep 1, Day1

description: 10x Genomics

value: female


title: distal_colon_day_7_replicate_4

description: colon_clean_VST_counts.csv column 49


title: distal_colon_day_21_replicate_7

description: colon_clean_VST_counts.csv column 53


title: Wild Type Rep 2 [WT2_S2]

city: Bethesda

first: Eric

last: Dang

state: Maryland

address: 9000 Rockville Pike

department: NIAID

institute: NIH

description: 10x Genomics

data_processing:
Counts were generated using cellranger v6.0.0. Analysis was performed using Seurat V4 following the “Fast integration using reciprocal PCA (RPCA)” script. Dimensionality of 8 was determined by examining the Jackstraw and Elbow plots and a resolution of 0.2 was used. Cells were clustered by using the non-linear dimensional reduction technique, UMAP, in Seurat. For quality control measures, cells with features >200 and <5000 and <12.5% mitochondrial genes were excluded. The Tfh cluster was defined by expression of Pd1, Cxcr5, Bcl6, Icos, Ascl2, Tox2, Il4 and Il21. Exhausted T cells (ETC) were identified by expression of Icos, Ctla4, and downregulation of the activation markers, Cd69, Tcf7 and Lef1. Tregs were identified by Ccr9, Foxp3, Ahr, and Il10 expression. The T helper 1 (TH1) cluster was defined by the expression of Nkg7, Eomes, and Tnfrsf9 which encodes for 4-1BB. The Early Memory T cell (EMTC) cluster was defined based on expression of activation markers Cd69, Tcf7, Lef1 and Cd44. Two clusters not expressing CD4 or CD3 were also excluded from analysis. Pathway analysis between the clusters were performed using the ReactomeSGA R package
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, HTO barcode reference csv files

source_name: Peyers patches

extract_protocol:
Peyers patches were collected, CD4+ T cells bead purified (Miltenyi Biotec) and CD45.2+CD45.1-CD4+CD8-TCRβ+ OTII T cells were sorted on FACS ARIA
scRNA-seq libraries were made using a Chromium Single Cell 3′Library & Gel Bead Kit v2 (P/N 120737, 10x Genomics) and sequenced

value: wild type

value: CD4+ T cells

value: Peyers patches


title: Male sham sedentary biol rep1, Day1

description: 10x Genomics

value: Swiss Webster


title: Skin, week 1, 17°C, fish 17

description: fish 17

value: week 1


title: SRL3_DMSO_C_S21_RNA-seq


title: Wild Type Rep 1 [WT1_HTO_S1]

description: 10x Genomics


title: distal_colon_day_5_replicate_10

description: colon_clean_VST_counts.csv column 51


title: distal_colon_day_5_replicate_9

description: colon_clean_VST_counts.csv column 50


title: SRL3_DMSO_A_S19_RNA-seq


title: Wild Type Rep 2 [WT2_HTO_S2]

description: 10x Genomics


title: Skin, week 8, 12°C, fish 75

description: fish 75


title: STB1_3IAA_A_S34_RNA-seq


title: Skin, week 8, 12°C, fish 74

description: fish 74


title: TgfbrIWT/mut Rep 2 [LDS2_S6]

description: 10x Genomics

value: TgfbrIWT/mut


title: Skin, week 8, 12°C, fish 73

description: fish 73


title: SRL3_3IAA_B_S23_RNA-seq


title: Skin, week 1, 17°C, fish 15

description: fish 15


title: TgfbrIWT/mut Rep 1 [LDS1_S4]

description: 10x Genomics


title: Skin, week 8, 12°C, fish 76

description: fish 76


title: distal_colon_day_12_replicate_8

description: colon_clean_VST_counts.csv column 45


title: SRL3_3IAA_A_S22_RNA-seq


title: SCNT-TE-WGBS-rep2

city: Shanghai

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

description: SCNT

library_source: genomic

data_processing:
The raw sequencing reads were trimmed by trim_galore with default parameters to remove low-quality bases and adapters in paired-end reads.
The remaining reads of were aligned to the Macaca fascicularis genome (macFas5) using Bismark with the parameter “--non_directional”.
After merging the pair end bam files of each sample into a single bam file, the single bam file was sorted.
Then, deduplication was performed using bismark.
The methylation level and coverage depth of each cytosine were extracted from the aligned reads with bismark_methylation_extractor.
The bedGraph files resulted from bismark_methylation_extractor was converted to BW files using bedGraphToBigWig software.
The resulted CpG_report.txt files containing DNA methylation levels were used to subsequent analysis in R.
Assembly: macFas5
Supplementary files format and content: The tab-delimited txt files containing the DNA methylation peaks of CpGs of the corresponding samples.

molecule: genomic DNA

organism: Macaca fascicularis

source_name: trophoblast

extract_protocol:
ICSI and SCNT trophoblast cells were seeded into lysis buffer by mouth pipette and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit.
Each replicates containing trophoblast cells obtained from 6~8 blastocysts were collected for the library construction. A small amount of unmethylated Lambda DNA (Promega, D152A) was added to each sample before bisulfite conversion to serve as spike-in controls for evaluating bisulfite conversion efficiency. After column-based purification, DNA was complemented with the random primer Preamp and Klenow polymerase (Enzymatics, P7010-HC-L). This random priming was repeated five times in total. Second strands were synthesized using another random primer, Adapter 2. Final libraries were generated after PCR amplification with the Illumina universal PCR primer and Illumina indexed primer, and were then purified using SPRI beads. Final libraries were subjected to paired-end 150 bp sequencing on a NovaSeq 6000 sequencer (Illumina) with PhiX spike-in control.

value: trophoblast

value: embryo trophoblast cells

value: SCNT


title: distal_colon_day_14_replicate_8

description: colon_clean_VST_counts.csv column 47


title: SCNT-TE-WGBS-rep1

description: SCNT


title: distal_colon_day_5_replicate_4

description: colon_clean_VST_counts.csv column 48

value: F


title: Wild Type Rep 1 [WT1_S1]

description: 10x Genomics


title: distal_colon_day_7_replicate_3

description: colon_clean_VST_counts.csv column 44


title: ICSI-TE-WGBS-rep2

description: ICSI

value: ICSI


title: Skin, week 1, 17°C, fish 16

description: fish 16


title: SOK2_DMSO_C_S27_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SOK2-3xV5 IAA7::URA3

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SOK2-3xV5 IAA7::URA3


title: Skin, week 1, 17°C, fish 13

description: fish 13


title: SOK2_3IAA_C_S30_RNA-seq


title: SOK2_DMSO_B_S26_RNA-seq


title: ICSI-TE-WGBS-rep1

description: ICSI


title: distal_colon_day_12_replicate_3

description: colon_clean_VST_counts.csv column 42


title: distal_colon_day_5_replicate_3

description: colon_clean_VST_counts.csv column 43


title: distal_colon_day_14_replicate_7

description: colon_clean_VST_counts.csv column 46

value: M


title: SOK2_3IAA_B_S29_RNA-seq


title: SOK2_DMSO_A_S25_RNA-seq


title: siHP1g_dex_replicate3

city: Lyon

first: Coralie

last: Poulard

address: 28 rue laennec

institute: CRCL

data_processing:
All libraries were mapped on the hg38 version of the human genome using Bowtie2 (Galaxy Version 2.4.2 Galaxy 0)
Count tables were prepared using Htseq-count (Galaxy version 0.9.1)
Differential gene expression analysis was performed with DESeq2 (Galaxy Version 2.11.40.7 galaxy1) using different thresholds
Differentially expressed genes were identified using a fold change cutoff when indicated and false discovery rate adjusted p-value >0.05
Assembly: hg38
Supplementary files format and content: comma separated file (csv) containing log2 fold change and FDR values for the comparisons made in the columns and each row representing a gene.

source_name: Breast

growth_protocol: Cells were maintained in DMEM high glucose containing 10% fetal bovine serum at 37°C and in 5% CO2

extract_protocol:
Total RNA was extracted using Trizol (Thermo scientific) and 3 replicates for each condition were performed.
cDNA libraries were prepared using the RNA-seq library prep kits with UDIs (Lexogen, Vienna Austria). Quality of the cDNA was assessed and RT-qPCR was performed for selected GR target genes as quality control. Standard illumina protocols were used to construct the library for sequencing.

treatment_protocol: MDA-MB-231 cells depleated for PRMT5 (siPRMT5), HP1g (siHP1g) or control (siNS) weren incubated with 100nM of dexamethasone (dex) or equivalent volume of vehicule ethanol for 8h.

value: Breast

value: Breast cancer cells


title: distal_colon_day_14_replicate_3

description: colon_clean_VST_counts.csv column 41


title: SOK2_3IAA_A_S28_RNA-seq

city: SEATTLE


title: distal_colon_day_12_replicate_2

description: colon_clean_VST_counts.csv column 40


title: SMP1_DMSO_C_S33_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SMP1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SMP1-3xV5 IAA7::URA3


title: siHP1g_eth_replicate3


title: distal_colon_day_9_replicate_9

description: colon_clean_VST_counts.csv column 39


title: SMP1_DMSO_B_S32_RNA-seq


title: siPRMT5_dex_replicate3


title: Skin, week 1, 12°C, fish 7

description: fish 7


title: Skin, week 1, 12°C, fish 6

description: fish 6


title: distal_colon_day_9_replicate_8

description: colon_clean_VST_counts.csv column 38


title: SMP1_DMSO_A_S31_RNA-seq


title: Skin, week 1, 12°C, fish 9

description: fish 9


title: Skin, week 1, 17°C, fish 12

description: fish 12


title: siPRMT5_eth_replicate3


title: Skin, week 1, 12°C, fish 11

description: fish 11


title: siNS_dex_replicate3


title: SMP1_3IAA_C_S36_RNA-seq


title: distal_colon_day_7_replicate_9

description: colon_clean_VST_counts.csv column 37


title: SMP1_3IAA_B_S35_RNA-seq


title: distal_colon_day_7_replicate_8

description: colon_clean_VST_counts.csv column 36


title: siHP1g_dex_replicate2


title: Skin, before trial, 8°C, fish 4

description: fish 4

value: before trial


title: siNS_eth_replicate3


title: Skin, before trial, 8°C, fish 2

description: fish 2


title: Skin, before trial, 8°C, fish 3

description: fish 3


title: Skin, week 1, 12°C, fish 10

description: fish 10


title: Wildtype D. vir. adult CNS, Hi-C rep2

city: Lausanne

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description:
assembly: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120751/suppl/GSE120751_Dvir_HiC.fa.gz
Hi-C library

data_processing:
FASTQ files were mapped to the reference genome using distiller v0.3.3 (https://github.com/open2c/distiller-nf). The following reference genomes were used: dm6 for Drosophila melanogaster and GSE120751_Dvir_HiC.fa.gz downloaded from ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120751/suppl/ for Drosophila virilis.
For each biological replicate, unique pairs of reads with MAPQ ≥ 30 on both sides were aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction using cooler v0.8.11 (https://github.com/open2c/cooler).
For each sample, unique pairs of reads with MAPQ ≥ 30 on both sides from all replicates were aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction using cooler v0.8.11 (https://github.com/open2c/cooler).
Supplementary files format and content: Multi-resolution cooler file format (mcool): unique pairs of reads with MAPQ ≥ 30 on both sides, aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction (cooler v0.8.11, https://github.com/open2c/cooler).

organism: Drosophila virilis

source_name: central nervous system

growth_protocol: standard Drosophila culture at 25°C

extract_protocol:
20 larval CNSs or 10 adult CNSs or 1 million FACS-purified nuclei per replicate were homogenized in RPMI supplemented with 10% fetal bovine serum with a micropestle. Cells were crosslinked then subjected to Hi-C, cutting with Csp6I and MseI restriction enzymes.
Illumina sequencing libraries were prepared with a standard protocol.

treatment_protocol: animals were not subjected to any particular treatment.

value: Wildtype

value: central nervous system

value: adult


title: SMP1_3IAA_A_S34_RNA-seq

first: Lakshmi

last: Mahendrawada

institute: Fred Hutchinson Cancer Center

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained from DESeq2 analysis


title: distal_colon_day_7_replicate_7

description: colon_clean_VST_counts.csv column 35


title: siHP1g_eth_replicate2


title: Wildtype D. vir. adult CNS, Hi-C rep1


title: SKO1_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SKO1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SKO1-3xV5 IAA7::URA3


title: siPRMT5_dex_replicate2


title: 19.12 417-1_3678

first: Igor

last: Yakovlev

state: --- Select a state ---

address: Hogskoleveien 8

institute: Norwegian Institute of Bioeconomy Research

description: CTTGTA(A)

data_processing:
Sequences were trimmed using the software trimmomatic (version 0.36)
Cytosine methylation levels were estimated using the software Bismark (version 0.17.0) (Krueger and Andrews, 2011), where the trimmed sequences were non-directionally aligned to the target sequences using the bowtie1 algorithm. The fraction of reads showing C to U conversions was calculated for all the interrogated cytosine positions in the genomic contexts CpG (cytosine preceding guanine), CHG and CHH (where H corresponds to A, T or C).
CLC Genomics Workbench v 22
Assembly: Genomic sequence information for each gene was extracted from version 1.0 of the Norway spruce genome (www. http://congenie.org/) and selected set of genes, presented in Epicapture_master_annotation_list_total with seqs.xlsx
Supplementary files format and content: Text file with results on the level of cytosine methylation per position, the output from a Bismark module called - ..._coverage2cytosine.CX_report. This is what had been used to run DMRcaller – the columns are <target sequence> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>. The target sequences presented in Epicapture_master_annotation_list_total with seqs.xlsx

organism: Picea abies

source_name: Bud

extract_protocol:
Total DNA was extracted from powdered tissue of several terminal buds detached from twigs without needles and some bud scales and grinded in liquid nitrogen with mortar and pestle. Total DNA was extracted using DNeasy Plant Mini Kit (Qiagen, Hilden, Germany, cat. no. 69104), according to the manufacturer’s instruction.
After DNA-shearing using a M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA, US), the DNA fragments were bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo Research Corp, Orange, CA, USA) and the libraries were made using SeqCap Epi Enrichment system (Roche, Basel, Switzerland), following the manufacturer´s instructions.
Targeted bisulfite sequencing

value: Bud

value: Vegetative

tag: date


title: SKO1_DMSO_B_S38_RNA-seq

address: 1100 FAIRVIEW AVE N


title: distal_colon_day_14_replicate_5

description: colon_clean_VST_counts.csv column 32


title: siPRMT5_eth_replicate2


title: Skin, before trial, 8°C, fish 1

description: fish 1


title: distal_colon_day_9_replicate_7

description: colon_clean_VST_counts.csv column 33


title: siNS_dex_replicate2


title: SKO1_3IAA_C_S42_RNA-seq


title: SKO1_DMSO_A_S37_RNA-seq


title: 19.12 413-1_3662

description: GGCTAC(A)


title: 19.12 43-1_3677

description: TAGCTT(A)


title: siNS_eth_replicate2


title: distal_colon_day_14_replicate_4

description: colon_clean_VST_counts.csv column 31


title: SKO1_3IAA_B_S41_RNA-seq


title: 19.12 715-1_3667

description: GATCAG(A)


title: distal_colon_day_12_replicate_7

description: colon_clean_VST_counts.csv column 30


title: siHP1g_dex_replicate1


title: 19.12 212-1_3668

description: ACTTGA(A)


title: SKO1_3IAA_A_S40_RNA-seq


title: 19.12 46-1_3669

description: CAGATC(A)


title: distal_colon_day_14_replicate_6

description: colon_clean_VST_counts.csv column 34


title: SKN7_DMSO_C_S51_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SKN7-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SKN7-3xV5 IAA7::URA3


title: 05.11 417-1_3678

description: GCCAAT(A)


title: distal_colon_day_14_replicate_2

description: colon_clean_VST_counts.csv column 28


title: siPRMT5_dex_replicate1


title: distal_colon_day_9_replicate_4

description: colon_clean_VST_counts.csv column 29


title: SKN7_DMSO_B_S50_RNA-seq


title: distal_colon_day_7_replicate_2

description: colon_clean_VST_counts.csv column 27


title: 05.11 413-1_3662

description: ACAGTG(A)


title: SKN7_DMSO_A_S49_RNA-seq


title: distal_colon_day_7_replicate_1

description: colon_clean_VST_counts.csv column 26


title: siPRMT5_eth_replicate1


title: distal_colon_day_12_replicate_6

description: colon_clean_VST_counts.csv column 25


title: SKN7_3IAA_C_S54_RNA-seq


title: 05.11 715-1_3667

description: TTAGGC(A)


title: 05.11 43-1_3677

description: TGACCA(A)


title: siNS_dex_replicate1


title: siHP1g_eth_replicate1


title: SKN7_3IAA_B_S53_RNA-seq


title: distal_colon_day_12_replicate_5

description: colon_clean_VST_counts.csv column 24


title: distal_colon_day_9_replicate_3

description: colon_clean_VST_counts.csv column 23


title: MDMs, C18:0 (16h), biol rep 3

city: LIEGE

first: Sylvie

last: Legrand-Poels

address: Avenue de l'Hôpital

department: GIGA

country: Belgium

institute: Uliege

data_processing:
The reads for each condition were mapped the human reference genome hg19 from UCSC using
TopHat2 version 2.0.7 and stored as BAM files. Differential expression values were evaluated using
Cufflinks 2.1.1 package.
Assembly: hg19
Supplementary files format and content: only one file.txt (matrix table) with htseq-gene-count  for each sample

source_name: Monocytes-derived macrophages (MDMs)

growth_protocol:
Monocyte-derived macrophages (MDMs) were generated by culturing freshly isolated monocytes in
RPMI 1640 with 20% heat-inactivated FBS and 100 ng/mL of human M-CSF premium grade for 7 days
at 37 °C under 5% CO2 atmosphere. On the day prior to MDMs treatment, M-CSF-containing medium
was replaced with new medium containing only 10% FBS.

extract_protocol:
Total RNA was extracted using High pure RNA isolation kit (Roche) according to manufacturer’s instruction.
RNA librairies were prepared for each group of MDMs with the Truseq stranded mRNA sample prep kit from Illumina, based on polyA selection of mRNAs.

treatment_protocol: MDMs were treated by BSA and C18:0 (100 µM) for 16 hours

value: Monocytes-derived macrophages (MDMs)


title: 05.11 212-1_3668

description: CGATGT(A)


title: SFP1_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-SFP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-SFP1


title: SKN7_3IAA_A_S52_RNA-seq


title: distal_colon_day_9_replicate_2

description: colon_clean_VST_counts.csv column 22

value: F


title: MDMs, C18:0 (16h), biol rep 2


title: 05.11 46-1_3669

description: ATCACG(A)


title: 18.09 417-1_3678

description: ATTCCT(T)


title: MDMs, C18:0 (16h), biol rep 1


title: distal_colon_day_9_replicate_6

description: colon_clean_VST_counts.csv column 21


title: MDMs, BSA (16h), biol rep 3

value: BSA (16h)


title: 18.09 413-1_3662

description: ACTGAT(A)


title: distal_colon_day_7_replicate_6

description: colon_clean_VST_counts.csv column 20


title: SFP1_DMSO_A_S19_RNA-seq


title: SFP1_DMSO_B_S20_RNA-seq


title: Stem, 1H after MS (control, no bending), rep1 (NS1HR1)

description:
read_counts.txt
gene_fpkm.txt

source_name: Whole stem

value: Whole stem

value: Wudu

value: WT

value: Control, no bending


title: MDMs, BSA (16h), biol rep 2


title: MDMs, BSA (16h), biol rep 1


title: SFP1_3IAA_C_S24_RNA-seq


title: distal_colon_day_7_replicate_5

description: colon_clean_VST_counts.csv column 19

value: M


title: SFP1_3IAA_B_S23_RNA-seq


title: 18.09 715-1_3667

description: CGTACG(T)


title: distal_colon_day_0_replicate_13

description: colon_clean_VST_counts.csv column 18


title: 18.09 43-1_3677

description: GAGTGG(A)


title: distal_colon_day_0_replicate_12

description: colon_clean_VST_counts.csv column 17


title: NCI-H660_H3K27ac_ChIP

first: Amina

last: Zoubeidi

address: 2660 Oak Street

institute: Vancouver Prostate Centre

data_processing:
Basecalling was performed by Illumina Real Time Analysis (RTA) v2.11.3 with default settings
Demultiplexing was perfoemed by Illumina bcl2fastq v2.20.0.422 using parameters --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --barcode-mismatch 1
Raw reads were aligned to the hg38 (human) reference genome using BWA-MEM software (version 0.7.17) with default parameters. Alignments with mapping quality less than 60 were filtered out (leaving only uniquely mapped reads) and subsequently sam files were converted to bam files using Samtools software (version 1.1.2).
Narrow peaks were called using MACS2 callpeak (version 2.2.7.1) with options -f BAMPE -g 2.9e9 --keep-dup=1 -B -q 0.05. Broad peaks were called using MACS2 callpeak (version 2.2.7.1) with options -f BAM --broad -g 2.9e9 --keep-dup 1 --broad-cutoff 0.05. Bedtools intersect (v2.28.0) program suite was used to generate shared (-wa -u -f 0.5 -F 0.5 -e) and unique (-v -f 0.5 -F 0.5 -e) peak set between samples.
Custom bashscript was used to modify the utilization of Deeptools (v2.30.0) program suite to generate normalized bigwig files.
HOMER (v4.11) program suite was used to annotate peaks and perform motif enrichment analysis.
Assembly: hg38

source_name: NCI-H660 Prostate cancer cell line (ATCC, CRL-5813)

growth_protocol: 16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum (Gibco #A3160701).

extract_protocol:
Cell lines were grown in media supplemented with 5% FBS (Gibco #A3160701) and processed for ChIP using either the Magna ChIP Kit (Millipore #17-10085) according to manufacturer’s instructions with the following antibody AR (5 µg, Cell Signaling #5153_CloneD6F11) or published protocol (PMID: 20680851) with the following antibody H3K27ac (10µg, ActiveMotif #39685).
For ChIP-seq, sequencing libraries (100 ng DNA per sample) were constructed using the KAPA library Prep Kit (Roche, Cat KK8510) with Illumina TruSeq indexes. Libraries were assessed for quality using gel electrophoresis and libraries passing quality control (e.g., no primer dimers) were quantified using the KAPA Library Quantification Kit for Illumina (Roche, Cat KK4824). Libraries were sequenced using the Illumina NextSeq 500 (75 bp single-end reads; cell lines).

treatment_protocol: 16D cells were treated with DHT (10nM)before being used for ChIP seq sample preparation.

value: de novo NEPC

tag: disease state

value: AR negative, NEPC


title: 18.09 46-1_3669

description: GTGGCC(T)


title: SFP1_3IAA_A_S22_RNA-seq


title: SFL1_DMSO_C_S57_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SFL1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SFL1-3xV5 IAA7::URA3


title: 16D_CRPC_H3K27ac_ChIP

source_name: 16D Prostate cancer cell line generated from mouse xenograft of LNCaP

value: ENZ-sensitive CRPC

value: AR positive, CRPC


title: SFL1_DMSO_B_S56_RNA-seq


title: 18.09 212-1_3668

description: GTTTCG(G)

value: Bud


title: distal_colon_day_0_replicate_10

description: colon_clean_VST_counts.csv column 16


title: 16D_CRPC_Input_(for H3K27ac ChIP)


title: SFL1_DMSO_A_S55_RNA-seq


title: distal_colon_day_0_replicate_9

description: colon_clean_VST_counts.csv column 15


title: 30.07 413-1_3662

description: GTCCGC(A)

value: Vegetative


title: 30.07 43-1_3677

description: CCGTCC(C)


title: SFL1_3IAA_C_S60_RNA-seq


title: distal_colon_day_9_replicate_5

description: colon_clean_VST_counts.csv column 13


title: 16D_CRPC_DHT_AR_ChIP


title: distal_colon_day_12_replicate_4

description: colon_clean_VST_counts.csv column 14


title: 16D_CRPC_DHT_Input


title: 30.07 417-1_3678

description: GTGAAA(C)


title: 30.07 715-1_3667

description: ATGTCA(G)


title: SFL1_3IAA_B_S59_RNA-seq


title: 30.07 212-1_3668

description: AGTTCC(G)


title: distal_colon_day_14_replicate_1

description: colon_clean_VST_counts.csv column 12


title: 16D_CRPC_AR_ChIP


title: SFL1_3IAA_A_S58_RNA-seq


title: distal_colon_day_12_replicate_1

description: colon_clean_VST_counts.csv column 11


title: NCI-H660_Input


title: 30.07 46-1_3669

description: AGTCAA(C)


title: 16D_CRPC_Input_(for AR ChIP)


title: SDD4_DMSO_C_S15_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 SDD4-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SDD4-3xV5 IAA7::URA3


title: SDD4_DMSO_B_S14_RNA-seq


title: 42D_ENZR_shROR2_Rep2_RNAseq

data_processing:
Base calling and de-multiplexing were performed using either bcl2fastq2 Conversion Software (v2.20) or bcl-convert (v3.8.4) with default parameters as per Illumina recommendation.
RNA-seq data processing was performed by sequencing facilty using Illumina RNA-Seq Alignment (BaseSpace Workflow) v1.1.0
Briefly, Read sequences were aligned to the hg19 human reference genome using STAR aligner v2.5.0b. Assembly and differential expression was estimated using Cufflinks software (version 2.2.1).
Assembly: hg19

source_name: 42D Prostate cancer cell line generated from mouse xenograft of LNCaP

growth_protocol: 16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum, 42D ENZ-resistant (ENZR) cells were cultured in RPMI-1640 media containing 5% fetal bovine serum supplemented with 10mM ENZ.

extract_protocol:
Total RNA was isolated from cell lines using TRIazol method (Rio et al., 2010).
Library constructions were performed using the NEBnext Ultra II Directional RNA Library Prep Kit (Cat E7760L) and NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat E7490L). Sequencing was performed on an Illumina NextSeq 500 (43x43 or 59 x 59 or 61 x 61 bp paired-end reads)

treatment_protocol: 16D cells in RPMI-1640 media containing CSS were treated with 10mM ENZ for 10 days and sample for RNA-seq was prepared. 16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum and ROR2 was knock down using short-hairpin (sh) RNA strategy and then treated with 10mM ENZ for 10 days and samples were prepared for RNA-seq. 16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum and ROR2 was overexpressed. The ROR2 was knock down using short-hairpin (sh) RNA strategy in 42D-ENZR to generate 42D-ENZR-shROR2 cell line before being used for RNA-seq sample preparation.

value: ENZ-resistant CRPC-NE

value: ROR2 knockdown with shRNA

value: AR positive, Neuro Endocrine like


title: 18.06 413-1_3662

description: GGCTAC(A)


title: 42D_ENZR_shROR2_Rep1_RNAseq


title: SDD4_3IAA_C_S18_RNA-seq


title: distal_colon_day_5_replicate_2

description: colon_clean_VST_counts.csv column 10

value: F


title: distal_colon_day_5_replicate_1

description: colon_clean_VST_counts.csv column 9


title: 18.06 43-1_3677

description: TAGCTT(A)


title: 16D_CRPC_OE_ROR2_Rep2_RNAseq

value: Castration Resistant Prostate Cancer (CRPC)

value: ROR2 over expression

value: Castration resistant


title: distal_colon_day_5_replicate_6

description: discarded during WGCNA network construction


title: SDD4_DMSO_A_S13_RNA-seq


title: 18.06 715-1_3667

description: GATCAG(A)


title: distal_colon_day_5_replicate_5

description: colon_clean_VST_counts.csv column 8


title: 16D_CRPC_shROR2_ENZ10days_RNAseq

value: ROR2 knockdown with shRNA, Enzalutamide for 10days


title: distal_colon_day_0_replicate_16

description: colon_clean_VST_counts.csv column 7

value: M


title: 18.06 212-1_3668

description: ACTTGA(A)


title: Co hMSC biol replicate 3

city: Jupiter

first: Christopher

middle: Lee

last: Haga

state: Florida

address: 130 Scripps Way, BldgA261A

department: Molecular Medicine

institute: UF Scripps Biomedical Research

data_processing:
CutAdapt adapter removal
HiSAT2 sequence alignment
featureCounts sequence assignment to genome
Assembly: hg19
Supplementary files format and content: tab delimited text file containing read counts for genomic features

source_name: bone marrow derived

extract_protocol:
Zymo RNA miniprep
NEBNext Ultra II Directional RNA kit

treatment_protocol: Human MSCs transduced with either PMSCV-pig-TWIST1 or empty vector control.

value: bone marrow derived

value: mesenchymal stem cell

value: Empty vector control


title: 18.06 417-1_3678

description: CTTGTA(A)


title: distal_colon_day_0_replicate_15

description: colon_clean_VST_counts.csv column 6


title: 13.06 417-1_3678

description: GCCAAT(A)


title: 16D_CRPC_CSS_ENZ10days_RNAseq

value: Enzalutamide for 10days


title: distal_colon_day_9_replicate_1


title: RTG3_DMSO_B_S38_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 RTG3-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 RTG3-3xV5 IAA7::URA3


title: 18.06 46-1_3669

description: CAGATC(A)

value: Bud


title: SDD4_3IAA_A_S16_RNA-seq


title: Co hMSC biol replicate 2


title: 16D_CRPC_OE_ROR2_Rep1_RNAseq


title: 13.06 413-1_3662

description: ACAGTG(A)

value: Vegetative


title: 13.06 43-1_3677

description: TGACCA(A)


title: Co hMSC biol replicate 1


title: distal_colon_day_0_replicate_14

description: colon_clean_VST_counts.csv column 5


title: 13.06 715-1_3667

description: TTAGGC(A)


title: TWIST1 hMSC biol replicate 3

value: TWIST1 overexpression


title: distal_colon_day_0_replicate_11

description: colon_clean_VST_counts.csv column 4


title: distal_colon_day_0_replicate_8

description: colon_clean_VST_counts.csv column 3


title: RTG3_3IAA_B_S41_RNA-seq


title: RTG3_DMSO_C_S39_RNA-seq


title: 13.06 414-1_3668

description: CGATGT(A)


title: distal_colon_day_0_replicate_7

description: colon_clean_VST_counts.csv column 2


title: TWIST1 hMSC biol replicate 1


title: RTG3_3IAA_A_S40_RNA-seq


title: distal_colon_day_0_replicate_6

description: colon_clean_VST_counts.csv column 1


title: TWIST1 hMSC biol replicate 2


title: RTG1_DMSO_C_S45_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 RTG1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 RTG1-3xV5 IAA7::URA3


title: RTG1_DMSO_B_S44_RNA-seq


title: proximal_colon_day_0_replicate_5

description: colon_clean_VST_counts.csv column 122


title: SDD4_3IAA_B_S17_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 SDD4-3xV5 IAA7::URA3


title: 13.06 46-1_3669

description: ATCACG(A)


title: OS52

city: Pittsburgh

first: Kurt

last: Weiss

state: PA

address: 5117 Centre Avenue

institute: University of Pittsburgh

data_processing:
from paired-end FASTQ files were mapped and quantified using k-mer–based quasi-mapping with seqBias and gcBias corrections (Salmon v1.1.0, 31-kmer index built from GRCh38 Ensembl v99 transcript annotations)
Transcript-level abundance estimates were collapsed to gene-level estimates using tximport
Gene-level counts or log2normCPM values were implemented for subsequent analyses
Differentially expressed genes (DEGs) between patient lung metastases samples and primary tumor patient samples were calculated using a paired or unpaired DESeq2 v1.24.0 differential gene expression analysis controlling for method of collection (biopsy vs. resection); design = ~ method of collection + condition (primary/met). DEGs were defined as genes with an absolute value fold change >= 1.5; FDR <= 0.01; and minimum TPM of 1 in at least 10% of the samples.
Gene ontology analysis was performed to determine biological processes represented in the upregulated and downregulated gene sets. We performed hierarchical clustering was performed by utilizing the heatmap.3 function (https://raw.githubusercontent.com/obigriffith/biostar-tutorials/master/Heatmaps/heatmap.3.R). AR expression across cell lines was examined using Cancer Cell Line Encyclopedia (CCLE) data
AR expression across cell lines was examined using Cancer Cell Line Encyclopedia (CCLE) data. Gene expression levels from processed RNA-seq of 1379 cell lines were obtained from CCLE along with the sample information containing primary disease types and subtypes for all samples (version DepMap Public 21Q2).
Median AR expression values and quartile ranges for primary diseases and bone subtypes were calculated in base R and plotted using ggplot2 v.3.3.5.
Pathway analyses were performed using Ingenuity Pathway Analysis (IPA) (Qiagen, v68752261). Cut-offs for Exp. Log ratio= -0.58 and 0.58 and FDR= 0.01.

source_name: metastatic tumor, lung

extract_protocol:
RNA was harvested using with the AllPrep DNA/RNA FFPE kit (Qiagen, Cat# 80234) according to the manufacturer’s instructions under sterile RNase/DNase-free conditions. Quality RNA integrity number scores, and fragment sizes (DV200 metrics) were obtained utilizing the Agilent 4200 TapeStation system (Agilent Technologies, Inc).
RNA libraries for RNA-seq were prepared using 40ng RNA according to Illumina’s TruSeq RNA Access Library Preparation protocol

treatment_protocol: Patients with osteosarcoma treated surgically between 2002 and 2016 were identified and formalin-fixed paraffin embedded (FFPE) archival samples from primary and metastatic tumors were obtained.

value: metastatic tumor, lung

tag: cancer type

value: osteosarcoma


title: RTG1_DMSO_A_S43_RNA-seq


title: RTG3_DMSO_A_S37_RNA-seq


title: 05.06 413-1_3678

description: ACTGAT(A)

tag: cell line


title: 05.06 43-1_3662

description: GAGTGG(A)

tag: cell type


title: OS54

source_name: primary tumor, femur

value: primary tumor, femur


title: RTG1_3IAA_B_S47_RNA-seq


title: proximal_colon_day_0_replicate_4

description: colon_clean_VST_counts.csv column 121

value: F


title: OS46

source_name: primary tumor, tibia

value: primary tumor, tibia


title: OS44

source_name: primary tumor, ilium

value: primary tumor, ilium


title: proximal_colon_day_0_replicate_2

description: colon_clean_VST_counts.csv column 119


title: proximal_colon_day_0_replicate_1

description: colon_clean_VST_counts.csv column 118


title: proximal_colon_day_0_replicate_3

description: colon_clean_VST_counts.csv column 120


title: OS49


title: 05.06 417-1_3662

description: ATTCCT(T)

source_name: Bud


title: 05.06 715-1_3667

description: CGTACG(T)


title: proximal_colon_day_21_replicate_4

description: colon_clean_VST_counts.csv column 115


title: OS40


title: proximal_colon_day_21_replicate_8

description: colon_clean_VST_counts.csv column 117

value: M


title: 05.06 212-1_3667

description: GTTTCG(G)


title: OS50


title: RTG1_3IAA_A_S46_RNA-seq


title: OS38


title: 06.05 43-1_3677

description: CCGTCC(C)


title: RTG1_3IAA_C_S48_RNA-seq


title: OS34


title: 05.06 414-1_3669

description: GTGGCC(T)


title: OS43


title: proximal_colon_day_9_replicate_10

description: colon_clean_VST_counts.csv column 116


title: 06.05 715-1_3667

description: ATGTCA(G)


title: ROX1_DMSO_C_S51_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 ROX1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 ROX1-3xV5 IAA7::URA3


title: ROX1_3IAA_B_S53_RNA-seq


title: ROX1_DMSO_B_S50_RNA-seq


title: OS33


title: 06.05 413-1_3662

description: GTCCGC(A)


title: ROX1_3IAA_A_S52_RNA-seq


title: proximal_colon_day_21_replicate_3

description: colon_clean_VST_counts.csv column 114


title: ROX1_DMSO_A_S49_RNA-seq


title: RME1_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 RME1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 RME1-3xV5 IAA7::URA3


title: proximal_colon_day_21_replicate_2

description: colon_clean_VST_counts.csv column 113


title: ROX1_3IAA_C_S54_RNA-seq


title: proximal_colon_day_21_replicate_1

description: colon_clean_VST_counts.csv column 112


title: 06.05 417-1_3678

description: GTGAAA(C)


title: proximal_colon_day_21_replicate_7

description: colon_clean_VST_counts.csv column 111


title: 06.05 414-1_3669

description: AGTCAA(C)


title: OS35

source_name: primary tumor, humerus

value: primary tumor, humerus


title: 20.03 417-1_3678

description: CTTGTA(A)


title: 06.05 212-1_3668

description: AGTTCC(G)


title: OS28


title: OS25

source_name: primary tumor, thigh

value: primary tumor, thigh


title: proximal_colon_day_5_replicate_10


title: proximal_colon_day_21_replicate_6

description: colon_clean_VST_counts.csv column 110


title: OS30

source_name: primary tumor, radius

value: primary tumor, radius


title: RME1_DMSO_B_S38_RNA-seq


title: RME1_3IAA_C_S42_RNA-seq


title: proximal_colon_day_21_replicate_5

description: colon_clean_VST_counts.csv column 109


title: siNS_eth_replicate1

source_name: Breast

value: Breast

value: Breast cancer cells


title: RME1_3IAA_B_S41_RNA-seq


title: 20.03 715-1_3667

description: GATCAG(A)

value: Bud

value: Vegetative


title: 20.03 413-1_3662

description: GGCTAC(A)


title: proximal_colon_day_7_replicate_4

description: colon_clean_VST_counts.csv column 108


title: OS20


title: proximal_colon_day_5_replicate_4

description: colon_clean_VST_counts.csv column 107


title: 20.03 43-1_3677

description: TAGCTT(A)


title: RME1_DMSO_A_S37_RNA-seq


title: OS16


title: RLM1_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-RLM1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-RLM1


title: proximal_colon_day_12_replicate_8

description: colon_clean_VST_counts.csv column 104


title: OS17


title: 20.03 212-1_3668

description: ACTTGA(A)


title: RTG3_3IAA_C_S42_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 RTG3-3xV5 IAA7::URA3


title: 20.03 46-1_3669

description: CAGATC(A)


title: RME1_3IAA_A_S40_RNA-seq


title: 18.02 712-1_3678

description: GCCAAT(A)


title: proximal_colon_day_14_replicate_7

description: colon_clean_VST_counts.csv column 105


title: proximal_colon_day_7_replicate_3

description: colon_clean_VST_counts.csv column 103


title: OS12

value: osteosarcoma


title: 18.02 45-1_3662

description: ACAGTG(A)


title: RLM1_DMSO_A_S19_RNA-seq


title: OS08


title: RLM1_3IAA_C_S24_RNA-seq


title: proximal_colon_day_12_replicate_3

description: colon_clean_VST_counts.csv column 101


title: 18.02 715-1_3667

description: TTAGGC(A)


title: 18.02 414-1_3668

description: CGATGT(A)


title: OS06


title: RLM1_3IAA_B_S23_RNA-seq


title: RLM1_3IAA_A_S22_RNA-seq


title: OS15

value: primary tumor, femur


title: proximal_colon_day_14_replicate_8

description: colon_clean_VST_counts.csv column 106


title: RLM1_DMSO_B_S20_RNA-seq


title: 18.02 46-1_3669

description: ATCACG(A)


title: Watters_25


title: RIM101_DMSO_C_S9_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 RIM101-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 RIM101-3xV5 IAA7::URA3


title: Watters_24


title: proximal_colon_day_12_replicate_2

description: colon_clean_VST_counts.csv column 99

value: F


title: RIM101_DMSO_B_S8_RNA-seq


title: SUC2:CO seedlings, 7DAG, ZT14 [SUC2-3]

city: Sevilla

first: Federico

last: Valverde

state: Sevilla

address: 49th Americo vespucio Avenue

department: Institute for Plant Biochemistry and Photosynthesis (IBVF)

country: Spain

institute: Spanish national research Council (CSIC)

data_processing:
FASTQC for quality control
Alignment of reads against TAIR10 reference genome using STAR
Quantification using featureCounts
limma+voom for differential gene expression analysis
Assembly: TAIR10
Supplementary files format and content: comma-delimited file containing raw counts per gene

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis thaliana plants were grown in long day conditions (16 light; 8h darkness) at 22 degrees in soil.

extract_protocol:
RNeasy Plant Mini Kit
Strand-specific (conducted at BGI Hong Kong)

value: seedling

value: SUC2:HA:CO (co-10)

value: Long Day


title: 18.02 43-1_3677

description: TGACCA(A)


title: SUC2:CO seedlings, 7DAG, ZT14 [SUC2-2]


title: Watters_12


title: RIM101_DMSO_A_S7_RNA-seq


title: Watters_22


title: OS03

source_name: primary tumor, lower leg

value: primary tumor, lower leg


title: RIM101_3IAA_C_S12_RNA-seq


title: proximal_colon_day_5_replicate_3

description: colon_clean_VST_counts.csv column 102


title: Watters_21

value: primary tumor, tibia


title: proximal_colon_day_7_replicate_8

description: colon_clean_VST_counts.csv column 96

value: M


title: Col-0 seedlings, 7DAG, ZT14 [Col-0-3]

value: WT


title: Watters_09

value: metastatic tumor, lung


title: proximal_colon_day_14_replicate_3

description: colon_clean_VST_counts.csv column 100


title: RIM101_3IAA_B_S11_RNA-seq


title: Col-0 seedlings, 7DAG, ZT14 [Col-0-2]


title: RIM101_3IAA_A_S10_RNA-seq


title: proximal_colon_day_9_replicate_7

description: colon_clean_VST_counts.csv column 94


title: Col-0 seedlings, 7DAG, ZT14 [Col-0-1]


title: RFX1_DMSO_C_S15_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 RFX1-3xV5 IAA7 mini degron ::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 RFX1-3xV5 IAA7 mini degron ::URA3


title: Watters_16


title: proximal_colon_day_5_replicate_8


title: Watters_15


title: proximal_colon_day_9_replicate_9

description: colon_clean_VST_counts.csv column 98


title: RFX1_DMSO_B_S14_RNA-seq


title: proximal_colon_day_7_replicate_9

description: colon_clean_VST_counts.csv column 97


title: proximal_colon_day_14_replicate_5

description: colon_clean_VST_counts.csv column 93


title: 35S:CO seedlings, 7DAG, ZT14 [35SCO-2]


title: SUC2:CO seedlings, 7DAG, ZT14 [SUC2-1]


title: Watters_07


title: RFX1_DMSO_A_S13_RNA-seq


title: proximal_colon_day_14_replicate_4

description: colon_clean_VST_counts.csv column 92


title: 35S:CO seedlings, 7DAG, ZT14 [35SCO-1]


title: Watters_08


title: RFX1_3IAA_C_S18_RNA-seq


title: proximal_colon_day_12_replicate_7

description: colon_clean_VST_counts.csv column 91


title: proximal_colon_day_14_replicate_6

description: colon_clean_VST_counts.csv column 95


title: RFX1_3IAA_A_S16_RNA-seq


title: Watters_01


title: Watters_06


title: Watters_13


title: RFX1_3IAA_B_S17_RNA-seq


title: proximal_colon_day_9_replicate_4

description: colon_clean_VST_counts.csv column 90


title: W1118 flies, Day 2, vehicle, rep6 [D2Vh3]

city: Houston

first: Andrew

middle: M

last: Pickering

state: tx

address: 6431 Fannin St

institute: UTHealth Houston

data_processing:
Basecalls were performed using Illumina bcl2fastq version 2.18.0.12
Raw FASTQ sequence files were aligned to the reference genome using STAR version 2.7.10a_alpha_220601 with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the STAR alignment BAM files using HTSeq-count version 0.12.3 with parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Ensembl Drosophila melanogaster BDGP6.32.Release107
Supplementary files format and content: tab delimited text file containing raw counts for each gene (Ensembl ID#) for each sample

organism: Drosophila melanogaster

source_name: Whole fly

growth_protocol: flies were maintained in an 24C incubator on 10% sugar/yeast food

extract_protocol: RNA was extracted by RNAeasy qiagen extraction kit

treatment_protocol: 1uM cycloheximide was mixed directly into food

value: Whole fly

value: Control


title: proximal_colon_day_14_replicate_2

description: colon_clean_VST_counts.csv column 89


title: W1118 flies, Day 2, vehicle, rep5 [D2Vh2]


title: W1118 flies, Day 2, vehicle, rep4 [D2Vh1]


title: proximal_colon_day_7_replicate_1

description: colon_clean_VST_counts.csv column 88


title: REB1_DMSO_120_C_S48_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-REB1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-REB1


title: Watters_03

source_name: metastatic tumor, lung


title: REB1_DMSO_120_B_S42_RNA-seq


title: W1118 flies, Day 2, vehicle, rep3 [D2Vh-3]


title: Watters_02


title: proximal_colon_day_12_replicate_6

description: colon_clean_VST_counts.csv column 87


title: 35S:CO seedlings, 7DAG, ZT14 [35SCO-3]


title: W1118 flies, Day 2, vehicle, rep2 [D2Vh-2]


title: proximal_colon_day_12_replicate_5


title: W1118 flies, Day 2, vehicle, rep1 [D2Vh-1]


title: W1118 flies, Day 2, cycloheximide, rep6 [D2Cx3]

value: Cycloheximide