title: cMYC_lucOSOE_Tp53KO_EV

city: Hong Kong

first: Carmen

middle: Oi Ning

last: Leung

state: Please Select

address: Hung Hom

department: Applied Biology and Chemical Technology

country: Hong Kong

institute: The Hong Kong Polytechnic University

description:
Library name: cMYC_lucOSOE_Tp53KO_EV
10X Chromium Next GEM 3’ v3 chemistry Single Cell kit

data_processing:
cellranger-5.0.1
Assembly: mm10
Supplementary files format and content: cMYC_lucOSOE_Tp53KO_EV_barcodes.tsv.gz
Supplementary files format and content: cMYC_lucOSOE_Tp53KO_EV_features.tsv.gz
Supplementary files format and content: cMYC_lucOSOE_Tp53KO_EV_matrix.mtx.gz
Supplementary files format and content: cMYC_lucOSOE_Tp53KO_Kras_barcodes.tsv.gz
Supplementary files format and content: cMYC_lucOSOE_Tp53KO_Kras_features.tsv.gz
Supplementary files format and content: cMYC_lucOSOE_Tp53KO_Kras_matrix.mtx.gz

source_name: liver tumor

extract_protocol:
Tumors were cut into small pieces in ice-cold perfusion buffer and transferred to gentleMACS C tubes with four rounds of dissociation in digestion buffer with 0.5 mg/ml Collagenase IV and 0.1 mg/ml DNaseI using gentleMACS dissociator according to the manufacturer’s instructions. The cell suspensions were passed through 70 µm cell strainers prior to loading to the Percoll gradient mix to create a gradient. After centrifugation, the pellets were subjected to red blood cell lysis and resuspended in 2% FBS-PBS FACS buffer. Isolated cells were stained with an anti-CD45-APC antibody  for 45 minutes on ice. LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit was used to exclude dead cells. Isolated cells were analyzed. CD45+ cells were sorted on a BD FASCAriaIII Flow Cytometer. The cells were gated on viability (without doublets via SSC-A SSC-H gating and dead cells) for subsequent scRNA-sequencing.
The sorted live CD45+ cells stored in ice-cold FACS buffer were immediately processed according to manufacturer’s instructions by encapsulation into single cell gel beads (GEMs) and unique molecular identifier (UMI) barcoding using the Chromium Next GEM 3’ v3 chemistry Single Cell kit (10× Genomics) at The Beijing Genomics Institute. Libraries were prepared and sequenced on a NovaSeq platform (Illumina)

value: liver tumor

value: tissue

value: immune cells


title: cMYC_lucOSOE_Tp53KO_Kras

status: Public on Sep 16 2025

type: SRA

description:
Library name: cMYC_lucOSOE_Tp53KO_Kras
10X Chromium Next GEM 3’ v3 chemistry Single Cell kit

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type


title: h- msi2-G252E asp1-WT::kanMX biol_rep_3

city: New York

first: Ana

middle: M

last: Sanchez

state: NY

address: 430 E 67th Street, RRL-865

department: Molecular Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Library name: msi2_G252E_biol_rep_3

library_source: transcriptomic

data_processing:
Base calls from Illumina NovaSeq X Plus (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2-2.1.0
Resulting SAM files were converted to BAM files using Samtools
Count files for individual replicated were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source 'ensembl')
Differential expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

source_name: Haploid

growth_protocol: Log phase cultures grown at 30˚C in YES medium

extract_protocol:
Hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the NEB Ultra II Directional RNA library prep plus PolyA isolation module kit according to manufacturer's protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq X-Plus instrument at the Weill Cornell Medicine Genome Core Facility (in New York).

value: Haploid

tag: growth condition

value: log phase culture, YES (Yeast Extract with Supplements)

tag: developmental stage

value: haploid

tag: genotype


title: HEK293T-PRPS1-HA-dTAG, DMSO, rep2

city: Chicago

first: SHASHANK

last: SRIVASTAVA

state: IL

address: 303 E Superior St, SQE Lab 7-400

institute: Northwestern University

description: Library name: CONTROL_REP2

library_source: genomic

data_processing:
Data was processed using the nf-core/atacseq pipeline (https://nf-co.re/atacseq/2.1.2)
Base calls were performed using bcl2fastq2.20 for HiSeq output
Demultiplexed fastq files were trimmed according to trailing quality scores with TrimGalore and then reads were aligned to GRCh38 with BWA
Bigwig files were produced using bedtools
Assembly: GRCh38
Supplementary files format and content: bigWig for each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: NA, cell line used

extract_protocol:
Transposition was conducted with Tagment DNA Enzyme and Buffer Kit from Illumina and purified using Qiagen MinElute Reaction Cleanup Kit
ATAC seq. Transposed DNA was PCR amplified and library prepped using Nextera adaptors from Illumina

treatment_protocol: DMSO or 500nM dTG47 treatment for 24 hours, cells collected for ATAC seq

value: NA, cell line used

value: epithelial

tag: treatment

value: DMSO


title: Jejunum, Naproxen+Tryptophan, Experimental batch 4, Rep 05

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

description:
Library name: Jejunum_Naproxen+Tryptophan_Exp4_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

data_processing:
FASTQ files from multiple lanes were merged for each sample using the unix 'cat' command.
Salmon (v1.9.0) was used to quantify transcript reads counts from the merged FASTQ files against v102 of the Ensembl mouse annotation. The Salmon index used for these analyses included transcript sequences from the ‘Mus_musculus.GRCm38.cdna.all.fa’ (all Ensembl transcripts, excluding non-coding RNAs) and ‘Mus_musculus.GRCm38.ncrna.fa’ (non-coding RNAs) FASTA files, both of which were downloaded from the Ensembl ftp site. The full DNA sequence from the primary genome assembly (GRCm38; also downloaded from Ensembl) was also included in the Salmon index as a decoy. Salmon was run to account for sequence, GC, and positional biases using the following command line parameters: "--seqBias --gcBias --posBias". Additionally, Salmon was run with the selective alignment mapping strategy ("--validateMappings") and the Inward Stranded Reverse LIBTYPE ("-l ISR").
Salmon transcript counts were imported into R (v4.2.2) and summarized to gene level quantifications with the tximeta package (v1.16.0).
Assembly: GRCm38
Supplementary files format and content: salmon_gene_quants.txt is a tab-delimited text file containing unnormalized salmon gene-level read counts for each gene in each sample (gene x sample format). The first two columns contain the Ensembl gene ID and common gene symbol for each gene in the table. The remaining columns contain gene counts for each sample in the study.

molecule: total RNA

source_name: Jejunum

growth_protocol: Six-week-old C57BL/6 mice were obtained from the Jackson Laboratory and allowed to acclimatize for two weeks. Animals were kept in a 12-hour day/night cycle and had ad libitum access to food and water.

extract_protocol:
At the end of the treatment period, mice were sacrificed via CO2 asphyxiation and their whole heart and jejunum tissue were dissected, chopped into small pieces, and snap frozen in liquid nitrogen. Jejuna were flushed with PBS to remove fecal matter prior to chopping and freezing. RNA was extracted from whole heart or 30 mg of jejunum using the Promega Maxwell RSC simplyRNA Tissue Kit (AS1340).
Libraries for each sample were constructed from 400 ng of total RNA using either the Illumina TruSeq Stranded mRNA library prep kit (heart) or the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (jejunum). Jejuna RNA samples were processed with a ribo-depletion based library prep kit because they had RIN scores < 8.

treatment_protocol: Mice were randomly assigned to treatment groups (n=8 per group). For three weeks, mice from the "control" and "tryptophan" groups received normal chow, while mice in the "celecoxib", "naproxen", and "naproxen+tryptophan" groups received chow supplemented with either celecoxib (550 ppm for females) or naproxen (1323 ppm for females; 1610 ppm for males). During the third and final week of the dietary exposure, mice in the "tryptophan" and "naproxen+tryptophan" groups received i.p. (intraperitoneal) injections of 50 mg/kg of tryptophan in PBS (phosphate buffered saline), while mice in the "control", "celecoxib", and "naproxen" groups received i.p. injections of PBS. Injections were administered daily at noon. Mice from the first experimental batch (Exp1) did not receive any injections.

value: Jejunum

tag: strain

value: Naproxen+Tryptophan

tag: Sex

value: Female

tag: age

value: 11 weeks

tag: experimental batch

tag: animal id

tag: dissection batch

tag: rrna removal_method

value: Ribo-Zero Plus

tag: library prep_kit

tag: index barcode

value: CGTCTGCG-ATTGTGAA


title: ABI027

type: genomic

city: Eiheiji-cho, Yoshida-gun

first: Shota

last: Nishitani

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

department: Research Center for Child Mental Development

country: Japan

institute: University of Fukui

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
minfi
normalized Average Beta (ssNoob)

label: Cy5 and Cy3

source_name: Adolescent Brain Imaging

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the prepIT®•L2P reagent (DNA Genotek).

value: saliva

tag: gender

value: male

tag: group

value: typically developing

tag: nationality

value: Japanese


title: h- biol_rep_3.

description: Library name: WT_biol_rep_3

tag: tissue

value: WT


title: Jejunum, Naproxen+Tryptophan, Experimental batch 4, Rep 04

description:
Library name: Jejunum_Naproxen+Tryptophan_Exp4_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: GTGAATAT-GAATGAGA


title: HEK293T-PRPS1-HA-dTAG, DMSO, rep1

description: Library name: CONTROL_REP1

tag: cell line

tag: cell type


title: xrna_1051_rep1

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

description: Library name: rna_1051_rep1

data_processing:
Read trimming (trimmomatic – for short reads, and porechop + nanofilt – for long reads
short read alignment (using hisat2 on RNA-seq reads, and bowtie2 – for ChIP-seq reads)
counting of exon-spanning reads with featureCounts (for RNA-seq)
calling enriched genomic regions with MACS2 (for ChIP-seq)
de novo genomic assembly with Flye (for long Nanopore reads)
Supplementary files format and content: featureCounts expression matrix (RNA-seq), MACS2-called peaks in broad mode (ChIP-seq)

organism: Drosophila virilis

source_name: ovary

extract_protocol:
Females of the 101 and 1051.47 strains were collected for DNA extraction and aged for 10-15 days. Genomic DNA was isolated from thirty pairs of ovaries using high-salt denaturing buffer containing 100 mM Tris-HCl (pH = 8), 10 mM EDTA (pH = 8), 350 mM NaCl, 2% SDS, and 7 M Urea following phenol-chloroform extraction. Before sequencing, we performed a size selection of high molecular weight DNA by depleting short DNA fragments below 10 kb using the Short Read Eliminator Kit (Circulomics, USA)
The preparation of DNA libraries for sequencing was carried out using the 1D ligation SQK-LSK109 kit (Oxford Nanopore Technologies (ONT), UK), by the recommended protocol from ONT. Sequencing was performed on a flow cell FLO-MIN-106D r9.4 (ONT, UK). The result was an average of 9.5 billion bases sequenced, with a median length of sequenced fragments from 20 to 40 kb for different libraries.

value: ovary

tag: batch


title: ABI026

value: child maltreatment


title: h- biol_rep_2.

description: Library name: WT_biol_rep_2

value: Haploid

tag: growth condition

value: log phase culture, YES (Yeast Extract with Supplements)

tag: developmental stage

value: haploid

tag: genotype


title: ABI025

tag: age


title: Thim_rep3

city: GuangZhou

first: Zeng

last: Jun Xiang

address: No. 1023–1063 South Shatai Road, Baiyun District

country: China

institute: The Southern of Medical University

description: Library name: sample6

data_processing:
Seuqence read were trimmed for adaptor sequence/low-quality sequence using trim_galore(defalut parameter)
Trimmed sequence reads were mapped to GRCm39 using HISAT2(version:2.2.0)
The gene expression level for each sample was calculated with Stringtie2(version:2.1.7)
Assembly: GRCm39
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Tumor

extract_protocol:
RNA was harvested using TRIzol® Reagent(Invitrogen). 1.3ug of total RNA was used for the construction of seuqencing of sequencing libraies
RNA libraries for RNA-seq were prepared using TruseqTM RNA sample prep Kit following manufacturer's protocols

value: Tumor

tag: treatment

value: Thim


title: Thim_rep2

description: Library name: sample5


title: ABI024


title: h- biol_rep_1.

description: Library name: WT_biol_rep_1


title: Jejunum, Naproxen+Tryptophan, Experimental batch 4, Rep 01

description:
Library name: Jejunum_Naproxen+Tryptophan_Exp4_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

tag: strain

value: Naproxen+Tryptophan

tag: Sex

value: Female

value: 11 weeks

tag: experimental batch

tag: animal id

value: TGGCCGGT-GCGCTCTA


title: Thim_rep1

description: Library name: sample4


title: H3K27me3_AEBP2KO_Rep3

city: Dublin 2

first: Adrian

middle: P.

last: Bracken

state: Co. Dublin

address: Smurfit institute of Genetics, Lincoln Place, Trinity College Dublin

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
ChIP-Seq and Cut&Run reads quality was confirmed by fastqc, then high-quality reads aligned to reference mouse genome (mm10) by bowtie2. ChIP-Rx reads were aligned to a metagenome mm10_hg38 by bowtie2. PCR duplicate reads were removed by Picard. RNA-Seq fastqs of WT ESCs were aligned to mm10 using STAR and bigwigs were generated using deepTools bamCoverage for visualisation in UCSC Genome Browser.
The duplicates-removed spike-in bam files mapped reads number was counted and used for generating the normalization factor (a), for ChIP-Rx samples. Generally, normalization factor (a) was calculated by 1 divide the spike-in genome bam file reads count. (Orlando, et al 2014)
For UCSC genome browser visualization, ChIP-Seq and Cut&Run bigwigs were generated by BamCoverage at 10 bp resolution and using RPKM normalization. ChIP-Rx bigwig files were generated with Rx normalization factor.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Run

source_name: E14 AEBP2 KO mESCs, H3K27me3 Cut&Run Rep3, matched for Fig.4 and Extended Fig.6

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatinized culture dishes in GMEM (Sigma) supplemented with 20% FBS (Gibco), 100U/mL Penicillin-Streptomycin (Gibco), 50 μM β-mercaptoethanol (Sigma), 1:100 GlutaMax, 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 1:500 homemade leukaemia inhibitory factor (LIF), and 2i components; 3 μM GSK inhibitor CHIRON99021 (Cayman) and 1 μM MEK inhibitor PD0325901 (Cayman).The ESCs were split and media was changed every 2 days. For EpiLC differentiation experiments, the dishes were coated with 16 μl/ml fibronectin for 2~3 hours. 2 million ESCs were washed three times with PBS and seeded on the fibronectin coated dished in NDiff227 medium (Takara) supplemented with 20 ng/ml Activin A (Peprotech), 12 ng/ml bFGF (Gibco) and 1% Knockout Serum Replacement (KSR, Thermo) for 2 days. The EpiLC culture medium was changed daily.

extract_protocol:
For RNA-Seq: Cell pellets from WT ESCs were collected at different days (representing Replicates 1,2 and 3) and total mRNA extracted using the Qiagen RNeasy Mini Kit.
ChIP-Seq/Rx library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol. The CUT&RUN experiments were performed following the Epicypher CUT&RUN Protocol v1.5.1. The Monarch PCR & DNA Cleanup Kit (New England Biolabs) protocol was used to purify the DNA. RNASeq Libraries were prepared by Novogene and sequenced using NovaSeq X Plus PE150.
Illumina NextSeq 500, 75-bp single end (rescues samples); NextSeq2000, 75-bp single end (AEBP2 KO ChIPs); NextSeq2000, 50-bp paired-end

treatment_protocol: No treatment applicable.

value: mouse embryonic stem cell

tag: antibody

value: H3K27me3 (Cell Signaling, C36B11)


title: Jejunum, Naproxen+Tryptophan, Experimental batch 4, Rep 03

description:
Library name: Jejunum_Naproxen+Tryptophan_Exp4_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: dissection batch

tag: rrna removal_method

value: Ribo-Zero Plus

tag: library prep_kit

tag: index barcode

value: TGCGAGAC-CAACAATG


title: T cells, PERK-KO, Ploy stimulation-2

city: Milwaukee

first: Qiao

middle: cheng

last: Cheng

state: Wisconsin

institute: Medical College of Wisconsin

description: Library name: Poly_PK2

data_processing:
The sequenced reads (raw reads) often contain low quality reads and adapters, which will affect the analysis quality. The raw reads were filtered as follows: (1) Remove reads containing adapters. (2) Remove reads containing N > 10% (N represents the base cannot be determined). (3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Assembly: Mouse mm10
Supplementary files format and content: raw_counts_All_Samples.txt

source_name: Spleen

growth_protocol: T cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using TRIZOL (invitrogen). 0.5ug of total RNA was used to construct sequence libraries.
First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: T cells were treated with anti-CD3 and anti-CD28 antibodies or allogeneic antigen presenting cells (APCs)

tag: tissue

value: Spleen

value: T cells

value: PERK-KO

value: Poly stimulation


title: ABI022

value: saliva

tag: gender

value: female

tag: group

value: child maltreatment

tag: nationality

value: Japanese


title: ABI023

value: typically developing


title: H3K27me3_SKO_Rep3

source_name: E14 AEBP2S KO mESCs, H3K27me3 Cut&Run Rep3, matched for Fig.4 and Extended Fig.6

tag: cell line

tag: cell type


title: Jejunum, Naproxen+Tryptophan, Experimental batch 4, Rep 07

description:
Library name: Jejunum_Naproxen+Tryptophan_Exp4_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

value: Naproxen+Tryptophan

tag: age

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: CCATTCGA-CGGACAAC


title: PBS_rep2

description: Library name: sample2

value: Tumor

tag: genotype

value: WT

tag: treatment

value: PBS

tag: batch


title: Jejunum, Naproxen+Tryptophan, Experimental batch 4, Rep 02

description:
Library name: Jejunum_Naproxen+Tryptophan_Exp4_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: strain

tag: Sex

value: Female

value: 11 weeks

tag: experimental batch

value: Ribo-Zero Plus

value: GACGTCTT-GGTGAACC


title: ABI021

value: male


title: PBS_rep3

description: Library name: sample3


title: h- msi2-G252E asp1-WT::kanMX biol_rep_1

description: Library name: msi2_G252E_biol_rep_1

value: Haploid

tag: growth condition

value: log phase culture, YES (Yeast Extract with Supplements)

tag: developmental stage

value: haploid


title: H3K27me3_LKO_Rep3

source_name: E14 AEBP2L KO mESCs, H3K27me3 Cut&Run Rep3, matched for Fig.4 and Extended Fig.6

value: mouse embryonic stem cell

tag: antibody

value: H3K27me3 (Cell Signaling, C36B11)


title: Jejunum, Tryptophan, Experimental batch 4, Rep 07

description:
Library name: Jejunum_Tryptophan_Exp4_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

value: Tryptophan

tag: animal id

tag: dissection batch

tag: rrna removal_method

tag: library prep_kit

tag: index barcode

value: ACGCACCT-CCTTCACC


title: ABI020

tag: tissue

value: saliva

tag: gender

tag: group

value: child maltreatment

tag: nationality

value: Japanese


title: jc6495_KPC_METS_FOXA1

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description:
FOXA1-KPC mets-Rep 2
KPC mets
FOXA1 METS

data_processing:
Reads were mapped to hg38 or mm10 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.  For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences. Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Assembly: GRCh38,GRCm38
Supplementary files format and content: bed/text

source_name: mouse pancreatic cancer cells

growth_protocol: HPAF-II & ASPC-1 cells were grown in MEM & RPMI High 10% FBS, Sodium pyruvate. KPC mouse cells were grown in DMEM 10% FBS

extract_protocol:
ChIP-Seq was performed at described in Ross-Innes CS et al. Nature. 2012. Antibodies used are specified above FOXA1-ab5089, HNF4G-atlas HPA005438, PRMT1-atlas HPA069769,H3K27Ac-ab4729,flag-sigma-F1804,GATA6-RD-AF1700
DNA was prepared for Illumina sequencing on the Nova Seq 6000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: untreated or CRISPR pertubation

value: Pancreatic adenocarcinoma

tag: genotype

value: WT

tag: treatment

value: untreated


title: PBS_rep1

description: Library name: sample1

value: Tumor

value: PBS

tag: batch


title: Jejunum, Tryptophan, Experimental batch 4, Rep 06

description:
Library name: Jejunum_Tryptophan_Exp4_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: strain

tag: Sex

value: Female

tag: age

value: 11 weeks

value: Ribo-Zero Plus

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: TATCGCAC-ACACTAAG


title: ABI019

value: male

value: typically developing


title: H3K27me3_AEBP2KO_Rep2

source_name: E14 AEBP2 KO mESCs, H3K27me3 Cut&Run Rep2, matched for Fig.4 and Extended Fig.6

tag: cell line

tag: cell type

value: mouse embryonic stem cell

value: H3K27me3 (Cell Signaling, C36B11)


title: H3K27me3_SKO_Rep2

source_name: E14 AEBP2S KO mESCs, H3K27me3 Cut&Run Rep2, matched for Fig.4 and Extended Fig.6

tag: antibody


title: ABI018

value: saliva


title: Jejunum, Tryptophan, Experimental batch 4, Rep 05

description:
Library name: Jejunum_Tryptophan_Exp4_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

value: Tryptophan

tag: experimental batch

tag: animal id

tag: dissection batch

value: GAACCGCG-TAAGGTCA


title: Jejunum, Tryptophan, Experimental batch 4, Rep 03

description:
Library name: Jejunum_Tryptophan_Exp4_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: rrna removal_method

tag: library prep_kit

tag: index barcode

value: CTGCTTCC-GATCTATC


title: Jejunum, Tryptophan, Experimental batch 4, Rep 02

description:
Library name: Jejunum_Tryptophan_Exp4_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: tissue

value: GCCACAGG-ATGGCATG


title: H3K27me3_WT_Rep2

source_name: E14 WT mESCs, H3K27me3 Cut&Run Rep2, matched for Fig.4 and Extended Fig.6


title: Jejunum, Naproxen+Tryptophan, Experimental batch 4, Rep 06

description:
Library name: Jejunum_Naproxen+Tryptophan_Exp4_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Naproxen+Tryptophan

value: GATCTATC-AGCCTCAT


title: H3K27me3_LKO_Rep2

source_name: E14 AEBP2L KO mESCs, H3K27me3 Cut&Run Rep2, matched for Fig.4 and Extended Fig.6


title: ABI017

tag: gender

tag: group

tag: nationality

value: Japanese


title: ABI016


title: H3K27me3_AEBP2KO_Rep1

source_name: E14 AEBP2 KO mESCs, H3K27me3 Cut&Run Rep1, matched for Fig.4 and Extended Fig.6

tag: genotype


title: Jejunum, Tryptophan, Experimental batch 4, Rep 01

description:
Library name: Jejunum_Tryptophan_Exp4_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: strain

tag: treatment

value: Female

value: 11 weeks

value: TTCCTGTT-AAGATACT


title: ABI015

value: female

tag: age

value: child maltreatment


title: H3K27me3_SKO_Rep1

source_name: E14 AEBP2S KO mESCs, H3K27me3 Cut&Run Rep1, matched for Fig.4 and Extended Fig.6

tag: cell line


title: Jejunum, Tryptophan, Experimental batch 4, Rep 08

description:
Library name: Jejunum_Tryptophan_Exp4_08
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: Sex

value: Ribo-Zero Plus

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: TTGCCTAG-TAAGTGGT


title: H3K27me3_WT_Rep3

source_name: E14 WT mESCs, H3K27me3 Cut&Run Rep3, matched for Fig.4 and Extended Fig.6

tag: cell type

value: mouse embryonic stem cell

tag: antibody

value: H3K27me3 (Cell Signaling, C36B11)


title: ABI014

value: saliva

value: typically developing


title: 2_HeLa_siVIM-270_OMe_2

type: RNA

city: Bunkyo-ku

first: Seongjin

last: An

state: Tokyo

department: Graduate School of Frontier Science

institute: The University of Tokyo

description: Gene expression

hyb_protocol: Cy3-labeled RNAs were fragmented using the Gene Expression Hybridization Kit (Agilent Technologies) and hybridized to a SurePrint G3 Human GE Microarray (version 3, 8 x 60 K) (Agilent Technologies) at 65℃ for 16 h.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (one color, scan resolution 3um, dye channel is set to Green).

data_processing: Signals were quantified by Feature Extraction version 12.1.1.1 (Agilent Techinologies).

label_protocol: cDNA and Cy3-labeled RNA were synthesized using the Quick Amp Labeling kit for One Color (Agilent Technologies).

growth_protocol: A HeLa cell suspension (0.5 x 10^5 cells/mL) was inoculated into a well of 24-well culture plate 1 day before transfection.

extract_protocol: Total RNA was purified using FastGene RNA Premium Kit (NIPPON Genetics) and the quality of the total RNA was confirmed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and a Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were transfected with 50 nM of each siRNA using 2 µL of Lipofectamine 2000 (Thermo Fisher Scientific). At 24 h post-transfection, cells were harvested from two wells per one sample.

value: HeLa

value: cervical cancer cells


title: Jejunum, Tryptophan, Experimental batch 4, Rep 04

description:
Library name: Jejunum_Tryptophan_Exp4_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

value: Tryptophan

tag: experimental batch

tag: animal id

value: CATAATAC-CGTTAGAA


title: ABI013

value: male

value: Japanese


title: Jejunum, Naproxen, Experimental batch 4, Rep 05

description:
Library name: Jejunum_Naproxen_Exp4_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Naproxen

value: Female

value: 11 weeks

tag: dissection batch

tag: rrna removal_method

value: TACTCATA-GCCACAGG


title: H3K27me3_WT_Rep1

source_name: E14 WT mESCs, H3K27me3 Cut&Run Rep1, matched for Fig.4 and Extended Fig.6


title: 2_HeLa_siVIM-270

description: Gene expression


title: H3K27me3_LKO_Rep1

source_name: E14 AEBP2L KO mESCs, H3K27me3 Cut&Run Rep1, matched for Fig.4 and Extended Fig.6


title: 2_HeLa_Mock

description: Gene expression


title: 2_HeLa_siVIM-270_Fluoro_2

description: Gene expression


title: ABI012

source_name: Adolescent Brain Imaging


title: 1_HeLa_siVIM-270_MOE_2

description: Gene expression


title: 1_HeLa_siVIM-270_MOE_4

description: Gene expression


title: 1_HeLa_siVIM-270_FA_4

description: Gene expression


title: Jejunum, Naproxen, Experimental batch 4, Rep 04

description:
Library name: Jejunum_Naproxen_Exp4_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

source_name: Jejunum

value: Ribo-Zero Plus

tag: library prep_kit

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

tag: index barcode

value: AGGTTATA-CGGAACTG


title: JARID2_AEBP2KO

data_processing:
ChIP-Seq and Cut&Run reads quality was confirmed by fastqc, then high-quality reads aligned to reference mouse genome (mm10) by bowtie2. ChIP-Rx reads were aligned to a metagenome mm10_hg38 by bowtie2. PCR duplicate reads were removed by Picard. RNA-Seq fastqs of WT ESCs were aligned to mm10 using STAR and bigwigs were generated using deepTools bamCoverage for visualisation in UCSC Genome Browser.
The duplicates-removed spike-in bam files mapped reads number was counted and used for generating the normalization factor (a), for ChIP-Rx samples. Generally, normalization factor (a) was calculated by 1 divide the spike-in genome bam file reads count. (Orlando, et al 2014)
For UCSC genome browser visualization, ChIP-Seq and Cut&Run bigwigs were generated by BamCoverage at 10 bp resolution and using RPKM normalization. ChIP-Rx bigwig files were generated with Rx normalization factor.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: E14 AEBP2 KO mESCs, JARID2 ChIP-Seq, matched for Fig.4 and Extended Fig.6

value: mouse embryonic stem cell

value: JARID2 (Cell Signaling, D6M9X)


title: 1_HeLa_siVIM-270_DNA_2

description: Gene expression


title: Jejunum, Naproxen, Experimental batch 4, Rep 03

description:
Library name: Jejunum_Naproxen_Exp4_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: tissue

value: AACTGTAG-TGCGGCGT


title: JARID2_SKO

source_name: E14 AEBP2S KO mESCs, JARID2 ChIP-Seq, matched for Fig.4 and Extended Fig.6


title: ABI010

value: saliva

tag: gender

tag: group

value: typically developing


title: ABI009

value: female

value: child maltreatment

tag: nationality


title: JARID2_LKO

source_name: E14 AEBP2L KO mESCs, JARID2 ChIP-Seq, matched for Fig.4 and Extended Fig.6

tag: genotype


title: Jejunum, Naproxen, Experimental batch 4, Rep 02

description:
Library name: Jejunum_Naproxen_Exp4_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

tag: strain

tag: treatment

value: ACTCGTGT-GTTCCAAT


title: Jejunum, Naproxen, Experimental batch 4, Rep 01

description:
Library name: Jejunum_Naproxen_Exp4_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: age

value: ATTGTGAA-GCAATGCA


title: s24 Lung tissue from control-CM rat

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
Library name: s24
s24 Lung tissue from control-CM rat

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 1.15 (adapter trimming)
FastQC v0.11.5 (quality control)
Rsubread v2.8.1 align
Rsubread v2.8.1 featureCounts
edgeR v3.36.0 TMM (normalization)
limma 3.50.0 (linearization)
Assembly: mRatBN7.2
Supplementary files format and content: tabular CPM TMM quantile normalized CPM (Count per Million)
Supplementary files format and content: genomic_B123P_processed_20_17913.tsv

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
RNAeasy Mini Kit (QIAGEN)
TruSeq Stranded Total RNA library prep kit (Illumina)

treatment_protocol: Lung tissues collected from 5 control-vehicle, 5 control-CM5480, 5 MCT-vehicle, 5 MCT-CM5480 rats.

value: Lung

tag: phenotype

value: Control

value: CM


title: ABI008

value: male

value: Japanese


title: Jejunum, Naproxen, Experimental batch 4, Rep 07

description:
Library name: Jejunum_Naproxen_Exp4_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Naproxen

tag: Sex

value: Female

value: 11 weeks

value: Ribo-Zero Plus

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: ACACTAAG-ATATGGAT


title: ABI007

value: saliva


title: 1_HeLa_siVIM-270_FA_2

description: Gene expression

tag: cell line

value: HeLa

tag: cell type

value: cervical cancer cells


title: SUZ12_AEBP2KO

description: 10% human NT2 cells was used for spike-in chromatin.

source_name: E14 AEBP2 KO mESCs, SUZ12 ChIP-Rx, matched for Fig.4 and Extended Fig.6

value: mouse embryonic stem cell

tag: antibody

value: SUZ12 (Cell Signaling, D39F6)


title: JARID2_WT

source_name: E14 WT mESCs, JARID2 ChIP-Seq, matched for Fig.4 and Extended Fig.6

value: JARID2 (Cell Signaling, D6M9X)


title: ABI006

value: typically developing


title: s23 Lung tissue from control-CM rat

description:
Library name: s23
s23 Lung tissue from control-CM rat

value: Lung

value: Control


title: Jejunum, Naproxen, Experimental batch 4, Rep 06

description:
Library name: Jejunum_Naproxen_Exp4_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

tag: experimental batch

tag: animal id

tag: dissection batch

value: CGGAACTG-TCGTAGTG


title: SUZ12_SKO

source_name: E14 AEBP2S KO mESCs, SUZ12 ChIP-Rx, matched for Fig.4 and Extended Fig.6


title: 1_HeLa_siVIM-270

description: Gene expression


title: SUZ12_LKO

source_name: E14 AEBP2L KO mESCs, SUZ12 ChIP-Rx, matched for Fig.4 and Extended Fig.6


title: s22 Lung tissue from control-CM rat

description:
Library name: s22
s22 Lung tissue from control-CM rat

value: CM


title: ABI011

value: female

value: child maltreatment

value: Japanese


title: Jejunum, Celecoxib, Experimental batch 4, Rep 08

description:
Library name: Jejunum_Celecoxib_Exp4_08
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Celecoxib

value: Female

value: 11 weeks

tag: rrna removal_method

value: Ribo-Zero Plus

tag: library prep_kit

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

tag: index barcode

value: TCTGTTGG-CCATTCGA


title: 1_HeLa_Mock

description: Gene expression

value: HeLa

value: cervical cancer cells


title: SUZ12_WT

source_name: E14 WT mESCs, SUZ12 ChIP-Rx, matched for Fig.4 and Extended Fig.6

value: mouse embryonic stem cell

value: SUZ12 (Cell Signaling, D39F6)


description:
Library name: s21
s21 Lung tissue from control-vehicle rat

tag: tissue

value: Lung

value: Control

value: Vehicle


title: ABI005

value: saliva

tag: gender

value: male

tag: group

tag: nationality


title: ABI004

value: female

value: typically developing


title: Jejunum, Celecoxib, Experimental batch 4, Rep 07

description:
Library name: Jejunum_Celecoxib_Exp4_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

tag: strain

tag: treatment

value: Celecoxib

value: CTCACCAA-TTGCCTAG


title: AEBP2_AEBP2KO

source_name: E14 AEBP2 KO mESCs, AEBP2 ChIP-Rx, matched for Fig.4 and Extended Fig.6

tag: genotype

value: AEBP2 (Cell Signaling, D7C6X)


title: ABI003

tag: age

value: child maltreatment

value: Japanese


title: Jejunum, Celecoxib, Experimental batch 4, Rep 05

description:
Library name: Jejunum_Celecoxib_Exp4_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: Sex

value: Female

value: 11 weeks

value: Ribo-Zero Plus

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: GGTCACGA-CATAATAC


title: Jejunum, Celecoxib, Experimental batch 4, Rep 06

description:
Library name: Jejunum_Celecoxib_Exp4_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: TCATCCTT-AGCTCGCT


title: s18 Lung tissue from control-CM rat

description:
Library name: s18
s18 Lung tissue from control-CM rat

value: Lung

tag: phenotype

value: Control

value: CM


title: ABI001

value: saliva

value: male


title: AEBP2_LKO

source_name: E14 AEBP2L KO mESCs, AEBP2 ChIP-Rx, matched for Fig.4 and Extended Fig.6

tag: cell line

tag: cell type

value: mouse embryonic stem cell

tag: antibody


description:
Library name: s15
s15 Lung tissue from control-vehicle rat

value: Vehicle


title: AEBP2_WT

source_name: E14 WT mESCs, AEBP2 ChIP-Rx, matched for Fig.4 and Extended Fig.6


title: s17 Lung tissue from control-CM rat

description:
Library name: s17
s17 Lung tissue from control-CM rat


title: Jejunum, Celecoxib, Experimental batch 4, Rep 02

description:
Library name: Jejunum_Celecoxib_Exp4_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

value: Celecoxib

tag: experimental batch

tag: animal id

tag: dissection batch

value: TCGATATC-ACTCGTGT


title: Jejunum, Celecoxib, Experimental batch 4, Rep 03

description:
Library name: Jejunum_Celecoxib_Exp4_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: rrna removal_method

tag: library prep_kit

tag: index barcode

value: AGTACTCC-AACAGGTT


description:
Library name: s14
s14 Lung tissue from control-vehicle rat

tag: tissue


title: TSC85

source_name: Toddler Social Cognition

extract_protocol: DNA was extracted using the QIAamp DNA Mini Kit (QIAGEN, Venlo, The Netherlands).

value: buccal epithelial

tag: gender

tag: days left at rt before the dna extraction

tag: group

value: typically developing

tag: nationality

value: Japanese


title: Jejunum, Celecoxib, Experimental batch 4, Rep 04

description:
Library name: Jejunum_Celecoxib_Exp4_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: strain

tag: treatment

value: Female

tag: age

value: 11 weeks

value: Ribo-Zero Plus

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: TGCGGCGT-TACCGAGG


title: TSC84

value: female


title: PC3 cells, c-Myc-CfaN transfection, replicate C

city: Jupiter

first: Ryan

middle: Raffaele

last: Milione

state: Florida

address: 130 Scripps Way, A-359

department: Chemistry

institute: UF Scripps Biomedical Research

description: Library name: pc3_CfaN_c

data_processing:
Samples 1-9 were analyzed together using the nf-core/rnasplice pipeline
Samples 7-15 were analyzed together using the nf-core/rnaseq pipeline
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
Supplementary files format and content: All processed data files are either bigwig, or TSV gene count files (salmon used for /rnasplice analysis, rsem used for /rnaseq analysis)
Supplementary files format and content: .tsv files contain raw counts for each sample
Supplementary files format and content: .bw files can be uploaded to IGV or UCSC to visualize tracks for each sample

source_name: Metastatic prostate cancer (AR-)

growth_protocol: All cells are cultured at 37C, 5% CO2 WPMY1 cells are cultured in DMEM + 10% FBS + 1% P/S LNCaP cells are cultured in RPMI1640 + 10% FBS + 1% P/S PC3 cells are cultured in DMEM F12 + 10% FBS + 1% P/S

extract_protocol:
RNA was harvested using Rneasy plus mini kit (Qiagen, 74134)
NEBNext rRNA depletion module and NEBNext Ultra II directional RNA library prep kit for Illumina

treatment_protocol: All transfections were performed with lipofectamine 3000 according to the manufacturer's instructions. Cells were harvested 24hr post-transfection.

value: Metastatic prostate cancer (AR-)

tag: cell line

tag: genotype

value: WT

value: c-Myc-CfaN, 0.75µg, 24h


description:
Library name: s13
s13 Lung tissue from control-vehicle rat

value: Lung

tag: phenotype

value: Control

value: Vehicle


description:
Library name: s19
s19 Lung tissue from control-vehicle rat


title: PC3 cells, c-Myc-CfaN transfection, replicate B

description: Library name: pc3_CfaN_b

tag: cell type


title: Jejunum, Control, Experimental batch 4, Rep 06

description:
Library name: Jejunum_Control_Exp4_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

tag: Sex

tag: experimental batch

tag: animal id

value: GTATGTTC-TTCCTGTT


title: s12 Lung tissue from MCT-CM rat

description:
Library name: s12
s12 Lung tissue from MCT-CM rat

value: MCT

value: CM


title: TSC82

value: buccal epithelial

value: male

value: typically developing

value: Japanese


title: PC3 cells, c-Myc-CfaN transfection, replicate A

description: Library name: pc3_CfaN_a


title: ABI002

value: saliva


title: s11 Lung tissue from MCT-CM rat

description:
Library name: s11
s11 Lung tissue from MCT-CM rat


title: s10 Lung tissue from MCT-vehicle rat

description:
Library name: s10
s10 Lung tissue from MCT-vehicle rat


title: PC3 cells, c-Myc-V5-6xHis transfection, replicate C

description: Library name: pc3_V5_c


title: TSC83


title: TSC81

value: child maltreatment


title: TSC80

value: female


title: s9 Lung tissue from MCT-vehicle rat

description:
Library name: s9
s9 Lung tissue from MCT-vehicle rat


title: PC3 cells, replicate C

description: Library name: pc3_c

value: Metastatic prostate cancer (AR-)


title: s7 Lung tissue from MCT-CM rat

description:
Library name: s7
s7 Lung tissue from MCT-CM rat


title: Jejunum, Control, Experimental batch 4, Rep 05

description:
Library name: Jejunum_Control_Exp4_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: 11 weeks

tag: dissection batch

tag: rrna removal_method

value: Ribo-Zero Plus

tag: library prep_kit

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: CGCTATGT-GTGTCGGA


title: AEBP2_SKO

description: 10% human NT2 cells was used for spike-in chromatin.

source_name: E14 AEBP2S KO mESCs, AEBP2 ChIP-Rx, matched for Fig.4 and Extended Fig.6

value: mouse embryonic stem cell

tag: antibody

value: AEBP2 (Cell Signaling, D7C6X)


title: TSC79

tag: tissue

tag: gender

tag: days left at rt before the dna extraction


title: Jejunum, Celecoxib, Experimental batch 4,Rep  01

description:
Library name: Jejunum_Celecoxib_Exp4_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

tag: strain

value: Celecoxib

tag: index barcode

value: GTGTCGGA-GCGCAAGC


title: Jejunum, Control, Experimental batch 4, Rep 04

description:
Library name: Jejunum_Control_Exp4_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: treatment

value: Control

tag: age

value: CTAGCGCT-GTCTACAC


title: Jejunum, Control, Experimental batch 4, Rep 03

description:
Library name: Jejunum_Control_Exp4_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: CATAGAGT-TGGTGGCA


title: TSC78

value: buccal epithelial

value: male

tag: group

tag: nationality

value: Japanese


title: Jejunum, Control, Experimental batch 4, Rep 02

description:
Library name: Jejunum_Control_Exp4_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: CAATTAAC-ATATCTCG


title: TSC77

value: female

value: typically developing


title: s6 Lung tissue from MCT-vehicle rat

description:
Library name: s6
s6 Lung tissue from MCT-vehicle rat

value: Lung

tag: phenotype

value: MCT

value: Vehicle


title: PC3 cells, replicate B

description: Library name: pc3_b

value: Metastatic prostate cancer (AR-)

tag: cell line

tag: cell type

tag: genotype

value: WT


title: Jejunum, Control, Experimental batch 4, Rep 01

description:
Library name: Jejunum_Control_Exp4_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Jejunum

tag: Sex

value: Female

value: 11 weeks

tag: experimental batch

tag: animal id

tag: dissection batch

value: Ribo-Zero Plus

value: Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: GTCTACAC-ACCTTGGC


title: PC3 cells, c-Myc-V5-6xHis transfection, replicate B

description: Library name: pc3_V5_b

tag: tissue


title: s5 Lung tissue from MCT-CM rat

description:
Library name: s5
s5 Lung tissue from MCT-CM rat

value: CM


title: Jejunum, Control, Experimental batch 4, Rep 08

description:
Library name: Jejunum_Control_Exp4_08
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Control

tag: rrna removal_method

tag: library prep_kit

value: TAAGGTCA-CTACGACA


title: TSC76

value: buccal epithelial

tag: gender

value: male

tag: days left at rt before the dna extraction

value: child maltreatment

value: Japanese


title: s3 Lung tissue from MCT-CM rat

description:
Library name: s3
s3 Lung tissue from MCT-CM rat

value: Lung

value: MCT

tag: treatment


title: PC3 cells, c-Myc-V5-6xHis transfection, replicate A

description: Library name: pc3_V5_a

value: Metastatic prostate cancer (AR-)


title: Jejunum, Control, Experimental batch 4, Rep 07

description:
Library name: Jejunum_Control_Exp4_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: strain

tag: age

tag: index barcode

value: AGCTCGCT-GATTCTGC


title: PC3 cells, replicate A

description: Library name: pc3_a

value: WT


title: TSC74

tag: group

tag: nationality


title: LNCaP cells, replicate C

description: Library name: lncap_c

source_name: Metastatic prostate cancer (AR+)

value: Metastatic prostate cancer (AR+)

tag: cell line

value: LNCaP

tag: cell type


title: TSC75

value: typically developing


title: s1 Lung tissue from MCT-vehicle rat

description:
Library name: s1
s1 Lung tissue from MCT-vehicle rat

tag: phenotype

value: Vehicle


title: LNCaP cells, replicate B

description: Library name: lncap_b

tag: genotype


title: Heart, Tryptophan, Experimental batch 3, Rep 04

description:
Library name: Heart_Tryptophan_Exp3_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

source_name: Heart

value: Heart

value: Tryptophan

tag: Sex

value: Female

value: 11 weeks

tag: experimental batch

tag: animal id

value: PolyA

value: Illumina TruSeq Stranded mRNA library prep kit

value: CAACAATG-CCGTGAAG


title: TSC73

tag: tissue

value: buccal epithelial

value: female

value: Japanese


title: Heart, Tryptophan, Experimental batch 3, Rep 03

description:
Library name: Heart_Tryptophan_Exp3_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: dissection batch

tag: rrna removal_method

tag: library prep_kit

value: GGTGAACC-TCCAACGC


title: TSC72

tag: gender

value: male

tag: days left at rt before the dna extraction

value: child maltreatment


title: s2 Lung tissue from MCT-vehicle rat

description:
Library name: s2
s2 Lung tissue from MCT-vehicle rat

value: Lung

value: MCT

tag: treatment


title: LNCaP cells, replicate A

description: Library name: lncap_a

value: Metastatic prostate cancer (AR+)

value: LNCaP

value: WT


title: WPMY1 cells, replicate C

description: Library name: wpmy1_c

source_name: Healthy prostate

value: Healthy prostate


title: Heart, Tryptophan, Experimental batch 3, Rep 01

description:
Library name: Heart_Tryptophan_Exp3_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

tag: strain

value: Tryptophan

value: Female

tag: age

tag: index barcode

value: GTTCGCCG-CAATGAGC


title: Heart, Tryptophan, Experimental batch 3, Rep 02

description:
Library name: Heart_Tryptophan_Exp3_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: 11 weeks

value: PolyA

value: Illumina TruSeq Stranded mRNA library prep kit

value: AACAGGTT-CTTGGTAT


title: s23 RV tissue from control-CM rat

description:
Library name: s23
s23 RV tissue from control-CM rat

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 1.15 (adapter trimming)
FastQC v0.11.5 (quality control)
Rsubread v2.8.1 align
Rsubread v2.8.1 featureCounts
edgeR v3.36.0 TMM (normalization)
limma 3.50.0 (linearization)
Assembly: mRatBN7.2
Supplementary files format and content: tabular CPM TMM quantile normalized CPM (Count per Million)
Supplementary files format and content: genomic_B123C_processed_20_16200.tsv

source_name: RV

treatment_protocol: RV tissues collected from 5 control-vehicle, 5 control-CM5480, 5 MCT-vehicle, 5 MCT-CM5480 rats.

value: RV

value: Control

value: CM


title: TSC71

value: buccal epithelial

value: female

tag: group

value: typically developing

tag: nationality

value: Japanese


title: WPMY1 cells, replicate B

description: Library name: wpmy1_b

tag: cell line

tag: cell type

value: WT


title: s24 RV tissue from control-CM rat

description:
Library name: s24
s24 RV tissue from control-CM rat

tag: phenotype


title: TSC70

value: male

value: child maltreatment


title: s22 RV tissue from control-CM rat

description:
Library name: s22
s22 RV tissue from control-CM rat


title: Heart, Tryptophan, Experimental batch 3, Rep 08

description:
Library name: Heart_Tryptophan_Exp3_08
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

value: Tryptophan

tag: Sex

tag: experimental batch

value: GCAATGCA-AACGTTCC


title: WPMY1 cells, replicate A

description: Library name: wpmy1_a

tag: tissue

value: Healthy prostate

tag: genotype


title: TSC69


title: ZNF207FL_Nterm_IP_Replicate 2

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: Maryland

address: 1050 Boyles Street

institute: National Cancer Institute

description: Library name: ZNF207FL_Nterm_IP_Replicate 2

data_processing:
Library Strategy: eCLIP-seq
UMI-tools was used to identify and segregrate the 5' UMI (Unique Molecular Identifier) sequences from the reads. Read adapters were trimmed with Cutadapt tool. Trimmed reads were mapped with STAR aligner in two steps: (1) First reads were mapped to repetitive DNA elements from human genome, (2) The unmapped reads from first mapping were used for the main alignment. The mapped reads were then deduplicated using UMI-tools based on the UMI sequences and the genomic alignment positions. The genomic coverage of the aligned reads were analyzed using deeptools. Peak calling was performed using HTSeq-CLIP and DEWSeq toos.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab delimited excel file with the enriched peak regions obtained with HTSeq-CLIP-DEWSeq pipeline (IP_D sample file has been annotated).

growth_protocol: HEK293 cells were maintained in Dulbecco’s Modified Eagle’s Medium (supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin).

extract_protocol:
Total RNA was extracted using RNeasy plus miniprep RNA isolation kit.
Library construction was performed following established protocols described previously (Van Nostrand et al., Methods Mol Biol, 2017).

treatment_protocol: Eight million cells were plated per cell line (FLAG-EGFP, FLAG-ZNF207 N-terminus, or ZNF207-FLAG C-terminus) in 15 cm cell culture dishes. After 24 hours, doxycycline was added to the media at a final concentration of 0.5 µg/mL to induce protein expression for 24 hours. Cells were washed twice with PBS and resuspended in 3 mL of PBS. UV-crosslinking was performed at 254 nm with an energy setting of 400 mJ/cm².

value: Human embryonic kidney cell line


title: s20 RV tissue from control-vehicle rat

description:
Library name: s20
s20 RV tissue from control-vehicle rat

value: Vehicle


title: Heart, Tryptophan, Experimental batch 3, Rep 07

description:
Library name: Heart_Tryptophan_Exp3_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: 11 weeks

tag: animal id

tag: dissection batch

tag: rrna removal_method

value: PolyA

value: Illumina TruSeq Stranded mRNA library prep kit

value: ATGGCATG-GGTACCTT


title: s21 RV tissue from control-CM rat

description:
Library name: s21
s21 RV tissue from control-CM rat

value: RV

value: Control

value: CM


title: Heart, Tryptophan, Experimental batch 3, Rep 06

description:
Library name: Heart_Tryptophan_Exp3_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: library prep_kit

value: GCGCAAGC-CGGCGTGA


title: ZNF207FL_Nterm_Input_Replicate 2

description: Library name: ZNF207FL_Nterm_Input_Replicate 2


title: Heart, Tryptophan, Experimental batch 3, Rep 05

description:
Library name: Heart_Tryptophan_Exp3_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: treatment

value: ATATGGAT-TAATACAG


title: s18 RV tissue from control-vehicle rat

description:
Library name: s18
s18 RV tissue from control-vehicle rat


title: Heart, Control, Experimental batch 3, Rep 03

description:
Library name: Heart_Control_Exp3_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: strain

value: CACGAGCG-TGGCAGAT


title: s19 RV tissue from control-vehicle rat

description:
Library name: s19
s19 RV tissue from control-vehicle rat


title: ZNF207FL_Nterm_Input_Replicate 1

description: Library name: ZNF207FL_Nterm_Input_Replicate 1


title: Heart, Control, Experimental batch 3, Rep 02

description:
Library name: Heart_Control_Exp3_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

tag: age

value: TGGTGGCA-TTACAGGA


title: s16 RV tissue from control-vehicle rat

description:
Library name: s16
s16 RV tissue from control-vehicle rat


title: s17 RV tissue from control-vehicle rat

description:
Library name: s17
s17 RV tissue from control-vehicle rat


title: ZNF207FL_Cterm_IP_Replicate 2

description: Library name: ZNF207FL_Cterm_IP_Replicate 2


title: TSC65

value: buccal epithelial

tag: gender

value: male

tag: days left at rt before the dna extraction

value: typically developing

value: Japanese


title: s13 RV tissue from control-CM rat

description:
Library name: s13
s13 RV tissue from control-CM rat


title: TSC64

value: female

tag: group

value: child maltreatment

tag: nationality


title: Heart, Control, Experimental batch 3, Rep 08

description:
Library name: Heart_Control_Exp3_08
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: 11 weeks

value: PolyA

tag: index barcode

value: ATATCTCG-ACTAAGAT


title: TSC66


title: Heart, Control, Experimental batch 3, Rep 01

description:
Library name: Heart_Control_Exp3_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Control

value: Illumina TruSeq Stranded mRNA library prep kit

value: GCGCTCTA-GTCGGAGC


title: TSC63


title: ZNF207FL_Cterm_Input_Replicate 2

description: Library name: ZNF207FL_Cterm_Input_Replicate 2

tag: cell line

tag: cell type

value: Human embryonic kidney cell line


title: s12 RV tissue from MCT-CM rat

description:
Library name: s12
s12 RV tissue from MCT-CM rat

value: RV

tag: phenotype

value: MCT

value: CM


title: Heart, Control, Experimental batch 3, Rep 07

description:
Library name: Heart_Control_Exp3_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: tissue

value: Heart

tag: Sex

tag: experimental batch

value: ACCTTGGC-ATGAGGCC


title: ZNF207FL_Cterm_IP_Replicate 1

description: Library name: ZNF207FL_Cterm_IP_Replicate 1


title: ZNF207FL_Nterm_IP_Replicate 1

description: Library name: ZNF207FL_Nterm_IP_Replicate 1


title: TSC62

value: buccal epithelial


title: TSC68

value: male

value: Japanese


title: TSC67

value: female

value: typically developing


title: s11 RV tissue from MCT-CM rat

description:
Library name: s11
s11 RV tissue from MCT-CM rat


title: Heart, Control, Experimental batch 3, Rep 06

description:
Library name: Heart_Control_Exp3_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: 11 weeks

tag: animal id

tag: dissection batch

value: GTTCCAAT-GCAGAATT


title: GFP_Control_IP_Replicate 2

description: Library name: GFP_Control_IP_Replicate 2


title: ZNF207FL_Cterm_Input_Replicate 1

description: Library name: ZNF207FL_Cterm_Input_Replicate 1


title: TSC61


title: Heart, Control, Experimental batch 3, Rep 05

description:
Library name: Heart_Control_Exp3_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Control

tag: rrna removal_method

value: PolyA

tag: library prep_kit

value: GGAGCGTC-GCACGGAC


title: TSC60

value: child maltreatment


title: GFP_Control_IP_Replicate 1

description: Library name: GFP_Control_IP_Replicate 1

value: Human embryonic kidney cell line


title: s9 RV tissue from MCT-vehicle rat

description:
Library name: s9
s9 RV tissue from MCT-vehicle rat

value: RV

value: MCT

tag: treatment

value: Vehicle


title: Heart, Control, Experimental batch 3, Rep 04

description:
Library name: Heart_Control_Exp3_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

tag: strain

tag: age

value: Illumina TruSeq Stranded mRNA library prep kit

value: AAGATACT-ATGTAAGT


title: s10 RV tissue from MCT-vehicle rat

description:
Library name: s10
s10 RV tissue from MCT-vehicle rat


title: GFP_Control_Input_Replicate 1

description: Library name: GFP_Control_Input_Replicate 1


title: Heart, Naproxen+Tryptophan, Experimental batch 2, Rep 08

description:
Library name: Heart_Naproxen+Tryptophan_Exp2_08
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Naproxen+Tryptophan

value: GTGTCGGA-GCGCAAGC


title: TSC58

value: buccal epithelial

tag: gender

value: male

tag: days left at rt before the dna extraction

value: Japanese


title: s8 RV tissue from MCT-vehicle rat

description:
Library name: s8
s8 RV tissue from MCT-vehicle rat


title: s7 RV tissue from MCT-CM rat

description:
Library name: s7
s7 RV tissue from MCT-CM rat

value: CM


title: Heart, Naproxen+Tryptophan, Experimental batch 2, Rep 07

description:
Library name: Heart_Naproxen+Tryptophan_Exp2_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: 11 weeks

value: GCCACAGG-ATGGCATG


title: TSC57

tag: group

value: typically developing

tag: nationality


title: Heart, Naproxen+Tryptophan, Experimental batch 2, Rep 06

description:
Library name: Heart_Naproxen+Tryptophan_Exp2_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: PolyA

tag: index barcode

value: TTGCCTAG-TAAGTGGT


title: PSA6_VDJ

city: London

first: Lucy

last: Durham

address: 1st Floor, New Hunt's House, Guy's Campus, Newcommen Street

department: Centre for Inflammation Biology and Cancer Immunology

institute: King's College London

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 6.1.1. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: .csv files containing VDJ information

source_name: Blood, synovial fluid, synovial tissue, skin

extract_protocol: Participant recruitment: Participants were recruited from Guy’s and St Thomas’ NHS Foundation Trust, London, UK. Participants donated synovial tissue (ST) and/or synovial fluid (SF) from an inflamed knee, one 6mm skin punch biopsy from lesional psoriasis and blood. Five patients donated ST by ultrasound guided needle biopsy during which 6-9 biopsies, each measuring ~1x1x2mm, were taken for this study. One patient (PsA 1) donated ST at the time of knee replacement surgery. Cell isolation: In the five patients where ST was obtained by ultrasound-guided needle biopsy, samples were processed immediately and cells were loaded onto the 10x Genomics chip within 8 hours of collection. Peripheral blood and SF mononuclear cells (PBMC and SFMC respectively) were isolated by density gradient centrifugation using LymphoprepTM (Axis-Shield, Oslo, Norway). ST biopsies were placed directly into serum-free RPMI media (Gibco, Grand Island, NY, USA) containing 0.3mg/ml Liberase and 0.1mg/ml DNase (both Roche, Basel, Switzerland) and processed using a custom 30-minute programme on the gentleMACS dissociator (Miltenyi Biotech, Bergisch Gladbach, Germany) which combines enzymatic and mechanical digestion to extract cells from tissue. Skin punch biopsies were incubated at 37°c in 10mg/ml Dispase II in Hanks Balanced Salt Solution (Gibco) for one hour. The epidermis was then peeled off and processed using the gentleMACS dissociator as described above for ST. In the patient where ST was obtained at knee replacement surgery, ST was minced into ~1-2mm3 sized pieces and PBMC and SFMC were isolated and skin epidermis separated from the dermis as described above. Samples were then cryopreserved in culture media containing 90% FCS (Gibco, Invitrogen, UK) and 10% DMSO (Fisher Scientific, Loughborough, UK) in liquid nitrogen until use. Upon thawing, all subsequent steps were the same as those described above. Sample staining: Samples were stained with fluorescently labelled, TotalSeqC and hashtag antibodies in the presence of Fc-receptor blocker (Biologend). Samples containing > 2x106 cells were stained in duplicate using different hashtags to enhance doublet detection. Prior to sorting, replicate cells from tissues stained with different hashtags were pooled, and DAPI (Thermo Fisher Scientific) was added. Fluorescent-Activated Cell Sorting: Memory T-cells (CD45RA-CD27+, CD45RA-CD27- and CD45RA+CD27-) were sorted on BD Aria cell sorter using an 85μm nozzle for ST and skin epidermis digests and a 70μm nozzle for PBMC and SFMC. Cells from all tissues were pooled and retained on ice pending library preparation.

tag: disease

value: psoriatic arthritis

tag: cell type

value: memory CD8+ T cells


title: TSC56

tag: tissue

value: female


title: s5 RV tissue from MCT-CM rat

description:
Library name: s5
s5 RV tissue from MCT-CM rat

value: RV

tag: phenotype

value: MCT


title: s3 RV tissue from MCT-CM rat

description:
Library name: s3
s3 RV tissue from MCT-CM rat


title: Heart, Naproxen+Tryptophan, Experimental batch 2, Rep 05

description:
Library name: Heart_Naproxen+Tryptophan_Exp2_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

value: Naproxen+Tryptophan

tag: Sex

tag: experimental batch

value: Illumina TruSeq Stranded mRNA library prep kit

value: AGCTCGCT-GATTCTGC


title: PSA6_GEX

description: 10x Genomics

value: Blood, synovial fluid, synovial tissue, skin


title: TSC55

value: buccal epithelial

value: male

value: child maltreatment

value: Japanese


title: s2 RV tissue from MCT-vehicle rat

description:
Library name: s2
s2 RV tissue from MCT-vehicle rat

value: Vehicle


title: TSC54

value: typically developing


title: s1 RV tissue from MCT-vehicle rat

description:
Library name: s1
s1 RV tissue from MCT-vehicle rat


title: PSA5_VDJ

description: 10x Genomics


title: TSC53


title: Heart, Naproxen+Tryptophan, Experimental batch 2, Rep 03

description:
Library name: Heart_Naproxen+Tryptophan_Exp2_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: 11 weeks

tag: animal id

tag: dissection batch

value: PolyA

value: AGTACTCC-AACAGGTT


title: duodenum_colon_female

city: Cleveland

first: Marissa

last: Scavuzzo

state: OH

address: 2109 Adelbert Rd

department: Genetics

institute: Case Western Reserve University

hyb_protocol: After thorough removal of the formamide, MERSCOPE custom gene probes were spotted onto the tissue sections and overlaid with parafilm. Dishes were sealed and incubated at 37oC for 36 hours. Post encoding probe hybridization, tissues were washed and prepared for gel embedding. First, probe mix was removed and replaced with 5mL of formamide wash buffer to incubate at 47oC for 30 minutes for two iterations. Slides were washed in wash buffer. During the second formamide incubation, gel coverslips (Vizgen, PN30200004) were cleaned with RNAse decontamination spray and ethanol before pre-treating with Gel Slick solution for 10 minutes. After washing the MERSCOPE slide with wash buffer, a gel embedding premix (Vizgen PN20300004) was prepared with 0.5% w/v ammonium persulfate solution and 0.05% N,N,N,N’-tetramethylethylenediamine and the slide was rinsed once in this solution before adding 50uL to the tissue section and covering with the Gel Slick-treated coverslip to evenly embed tissues into the gel. Gel was formed at room temperature for 1.5 hours before removing the coverslip and proceeding with tissue digestion with 1.5U/uL RNAse inhibitor (SUPERasin and Protector) in digestion premix (Vizgen PN20300005) at 37oC for 5 hours. Following digestion, tissues were cleared using SDS based clearing premix (Vizgen PN20300003) and 4U/mL Proteinase K (NEB, P8107) for 15 hours at 37oC before refreshing the solution and waiting 10 hours before switching to clearing premix without Proteinase K and storage at 37oC until imaging.

scan_protocol: MERFISH imaging was completed using Vizgen MERSCOPE Ultra Spatial Imaging platform. Imaging cartridge was thawed at 37oC for 60 minutes, wiped down to dry before cleaning with RNAse decontamination solution and ethanol. Clearing solution was removed from the tissue slides before washing twice with sample wash buffer. DAPI and PolyT staining was then done for 15 minutes rocking at room temperature protected from light, followed by a 10 minute incubation at room temperature with formamide wash buffer and a final wash in sample prep wash buffer. The MERSCOPE instrument fluidics were washed immediately preceding imaging. MERSCOPE slides were loaded into a clean flow chamber before chamber priming, tissue overview, high magnification imaging, and data acquisition.

data_processing:
Following data acquisition, segmentation parameters were selected and images were processed as output. We used a modified Seurat code to load data into R to support parquet files for cell boundary segmentation. Each individual animal and tissue region was processed, normalized using SCTransform, followed by principal component analysis prior to clustering. We mathematically defined the optimal principal components (PC) to use by calculating the percent variation associated with each. Next, we calculated the cumulative percentage for each PC and determined which exhibits greater than 90% cumulative percent and less than 5% variation associated with the PC. Next the difference between the variation of PC and subsequent PC was calculated where change of percentage of variation is more than 0.1% before finding the smaller of the two values as the optimal value for downstream analyses. Individual regions were combined by merging, and batch effects were removed using Harmony by grouping variables by original sample identity. Resolution was set at 0.1. Clustering was visualized by UMAP and differential gene expression was performed using Wilcoxon Rank Sum test. Visium spatial transcriptomics dataset was analyzed using the standard Visium HD Seurat pipeline. Briefly, data was loaded, normalized, and variable features were determined prior to clustering. Enteric glia were identified via unsupervised clustering and expression of a cohort of glial cell markers before subclustering enteric glia alone to assess spatial distribution and marker expression.
processed output of RNA counts from MERSCOPE

source_name: intestinal tissue

label_protocol: The parafilm-sealed dish holding the MERSCOPE slide in 70% ethanol was placed in the MERSCOPE Photobleacher (Vizgen PN10100003) for 5 hours at room temperature for autofluorescence quenching. Following quenching, slides were washed once in 1x PBS before they underwent cell boundary staining. Tissues were blocked at room temperature for 1 hour (Vizgen PN20300100) before primary staining (Vizgen PN20300010) with 1U/uL RNAse inhibitor for 1 hour at room temperature. Finally, tissues were stained with secondary staining solution (Vizgen PN20300011) with 1U/uL RNAse inhibitor for 1 hour at room temperature before washing 3x with 1x PBS and fixation at room temperature for 15 minutes. We next washed in PBS, washed with wash buffer (Vizgen PN20300001), and incubated in formamide wash buffer (Vizgen PN20300002) for 30 minutes at 37oC.

growth_protocol: Mice were housed at 22–24°C with a 12 hour light/12 hour dark cycle with standard chow (Lab Diet Pico Lab 5V5R, 14.7% calories from fat, 63.3% calories from carbohydrate, 22.0% calories from protein) and water provided ad libitum.

extract_protocol: Tissues were incubated for 3 hours in 4% PFA in 1x PBS at 4oC before transferring to 30% w/v sucrose in 4% v/v PFA in 1x PBS at 4oC for 16 hours. Tissues were washed in OCT, placed into RNAse free plastic cryomolds, and immediately frozen in dry ice. Tissues were transferred to -80oC for storage until further processing. All buffers and materials were prepared with RNAse-free reagents, including disinfection with RNAse decontamination solution and ethanol, and were pre-chilled. Tissues were equilibrated to -20oC in a Leica CM1950 cryostat for 20 minutes prior to mounting for sectioning. MERSCOPE frozen tissue slides were equilibrated to room temperature in parallel. Tissues were sectioned to trim away flanking tissue, collecting at least 3 tissues before and after into pre-chilled tubes for RNA isolation to measure DV200. To collect tissue onto MERSCOPE slides (Vizgen PN10500001), we sectioned at 10 m directly onto the room temperature MERSCOPE slide, holding the slide for 10 seconds for adhesion. The MERSCOPE slide with tissue was placed into a clean 60-mm petri dish and placed in the cryostat for 30 minutes for further adhesion. Slides were washed 3x with RNAse free 1x PBS, dried for 1 hour at room temperature, then overlaid with 70% ethanol to permeabilize the tissues. Dishes were secured with parafilm and placed at 4oC until further processing.

treatment_protocol: Upon euthanasia of 6 week old mice, the duodenum and colon were quickly collected, placed on ice in cold 4% v/v paraformaldehyde (PFA; Electron Microscopy Sciences, 15714) in 1x PBS, and flushed immediately with this solution to remove luminal contents.

value: female

value: duodenum and colon

value: 6-10 weeks


title: PSA5_CSP

description: 10x Genomics

value: psoriatic arthritis

value: memory CD8+ T cells


title: GFP_Control_Input_Replicate 2

description: Library name: GFP_Control_Input_Replicate 2

tag: cell line

value: Human embryonic kidney cell line


title: TSC52


title: TSC59


title: duodenum_colon_male


title: TSC51


title: rescues_WT_SUZ12

description: 10% human NT2 cells was used for spike-in chromatin.

source_name: E14 WT mESCs, SUZ12 ChIP-Rx

value: E14 WT mESCs, SUZ12 ChIP-Rx

value: mouse embryonic stem cell

tag: genotype

tag: antibody

value: SUZ12 (Cell Signaling, D39F6)


title: Heart, Naproxen, Experimental batch 2, Rep 07

description:
Library name: Heart_Naproxen_Exp2_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

tag: strain

tag: treatment

value: Naproxen

tag: age

tag: rrna removal_method

tag: library prep_kit

value: Illumina TruSeq Stranded mRNA library prep kit

value: AGGCAGAG-GGCATTCT


title: PSA6_CSP

description: 10x Genomics

value: Blood, synovial fluid, synovial tissue, skin


title: KO liver rep3

city: Vienna

first: Katharina

last: Schwertner

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University Vienna

description: Library name: Unknown_CL748-001T0018

data_processing:
Preprocessing and alignment by kallisto pipeline (Bray et al, 2016).
Assembly: GRCm38/mm10
Supplementary files format and content: csv file contains raw counts for each sample

source_name: liver

extract_protocol:
Total RNA was isolated from tissue using TRIzol reagent
VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605 was used to construct the mRNA libraries according to the protocol provided by Vazyme

value: liver


title: TSC50

value: buccal epithelial

tag: gender

value: male

tag: days left at rt before the dna extraction

tag: group

value: typically developing

tag: nationality

value: Japanese


title: rescues_WT_AEBP2

source_name: E14 WT mESCs, AEBP2 ChIP-Rx

value: E14 WT mESCs, AEBP2 ChIP-Rx

tag: cell type

value: AEBP2 (Cell Signaling, D7C6X)


title: TSC49

tag: tissue

value: child maltreatment


title: Heart, Naproxen+Tryptophan, Experimental batch 2, Rep 04

description:
Library name: Heart_Naproxen+Tryptophan_Exp2_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Naproxen+Tryptophan

tag: Sex

value: Female

value: 11 weeks

tag: experimental batch

value: PolyA

tag: index barcode

value: GTCTACAC-ACCTTGGC


title: gastrocnemius muscle from 18 months-old Pex-KO mice, KO_007

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of Pex5 knockout KO, biological rep7

data_processing:
Quality control of fastq files was performed by using fastqc  [1].
bbduk from bbtools [2] was used to remove adapters and low-quality tails from the reads, with the following parameters: k=13 ktrim=r useshortkmers=t mink=5 qtrim=rtrimq=10 minlength=20.
Then, trimmed and cleaned reads were aligned to the reference genome mm10 by using STAR [3], with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD.
Aligned reads were indexed with samtools [4].
Finally, number of reads mapping within genes was determined with htseq-count [5], run in intersection-nonempty mode.
[1] Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput SequenceData
[2] https://jgi.doe.gov/data-and-tools/software-tools/bbtools/
[3] Dobit, A. et al. (2013). STAR: ultrafast universal RNA-seq aligner
[4] Li, H. et al. (2009). The Sequence Alignment/Map format and SAMtools
[5] Putri, G. et al (2022). Analysing high-throughput sequencing data in Python withHTSeq 2.0
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: gastrocnemius muscle

growth_protocol: Mice were maintained on a 12-hour light/12-hour dark schedule and were fed standard rodent food chow and water ad libitum

extract_protocol:
Total RNA was extracted  from gastrocnemius muscle using TRIzol reagent (Life Technologies) following manufacturer's protocol
the QuantSeq 3' mRNA-seq Library Prep kit (Lexogen) was employed for library construction following manufacturer's protocol

treatment_protocol: Muscle-specific Pex5 ablation was achieved by crossing Pex5 floxed mice  with a transgenic line expressing Cre recombinase (CRE) under the control of Myosin Light Chain 1 fast promoter. Gastrocnemius muscle from 18 months-old mice was collected.

value: gastrocnemius muscle

value: 18 months-old


title: KO liver rep1

description: Library name: Unknown_CL748-001T0016


title: Heart, Naproxen, Experimental batch 2, Rep 05

description:
Library name: Heart_Naproxen_Exp2_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

data_processing:
FASTQ files from multiple lanes were merged for each sample using the unix 'cat' command.
Salmon (v1.9.0) was used to quantify transcript reads counts from the merged FASTQ files against v102 of the Ensembl mouse annotation. The Salmon index used for these analyses included transcript sequences from the ‘Mus_musculus.GRCm38.cdna.all.fa’ (all Ensembl transcripts, excluding non-coding RNAs) and ‘Mus_musculus.GRCm38.ncrna.fa’ (non-coding RNAs) FASTA files, both of which were downloaded from the Ensembl ftp site. The full DNA sequence from the primary genome assembly (GRCm38; also downloaded from Ensembl) was also included in the Salmon index as a decoy. Salmon was run to account for sequence, GC, and positional biases using the following command line parameters: "--seqBias --gcBias --posBias". Additionally, Salmon was run with the selective alignment mapping strategy ("--validateMappings") and the Inward Stranded Reverse LIBTYPE ("-l ISR").
Salmon transcript counts were imported into R (v4.2.2) and summarized to gene level quantifications with the tximeta package (v1.16.0).
Assembly: GRCm38
Supplementary files format and content: salmon_gene_quants.txt is a tab-delimited text file containing unnormalized salmon gene-level read counts for each gene in each sample (gene x sample format). The first two columns contain the Ensembl gene ID and common gene symbol for each gene in the table. The remaining columns contain gene counts for each sample in the study.

value: Heart

value: Naproxen

tag: animal id

tag: dissection batch

value: Illumina TruSeq Stranded mRNA library prep kit

value: CAATTAAC-ATATCTCG


title: gastrocnemius muscle from 18 months-old Pex-KO mice, KO_079

description: Transcriptome profile of Pex5 knockout KO, biological rep6

tag: genotype


title: TSC48

data_processing:
minfi
normalized Average Beta (ssNoob)

value: buccal epithelial

value: male


title: TSC47

value: Japanese


title: gastrocnemius muscle from 18 months-old Pex-KO mice, KO_072

description: Transcriptome profile of Pex5 knockout KO, biological rep5


title: WT liver rep3

description: Library name: Unknown_CL748-001T0015

value: liver


title: WT liver rep2

description: Library name: Unknown_CL748-001T0014


title: PSA5_GEX

description: 10x Genomics

value: Blood, synovial fluid, synovial tissue, skin

tag: disease

value: psoriatic arthritis

value: memory CD8+ T cells


title: gastrocnemius muscle from 18 months-old Pex-KO mice, KO_071

description: Transcriptome profile of Pex5 knockout KO, biological rep4


title: Heart, Naproxen, Experimental batch 2, Rep 03

description:
Library name: Heart_Naproxen_Exp2_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: strain

tag: treatment

value: Female

value: TTCCTGTT-AAGATACT


title: Heart, Naproxen+Tryptophan, Experimental batch 2, Rep 02

description:
Library name: Heart_Naproxen+Tryptophan_Exp2_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Naproxen+Tryptophan

tag: age

value: 11 weeks

tag: rrna removal_method

value: PolyA

value: TGCGGCGT-TACCGAGG


title: TSC46

tag: gender

value: female

value: typically developing


title: Heart, Naproxen+Tryptophan, Experimental batch 2, Rep 01

description:
Library name: Heart_Naproxen+Tryptophan_Exp2_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

tag: library prep_kit

value: Illumina TruSeq Stranded mRNA library prep kit

value: TGGTGGCA-TTACAGGA


title: TSC45

value: buccal epithelial

tag: days left at rt before the dna extraction

tag: group


title: Heart, Naproxen, Experimental batch 2, Rep 02

description:
Library name: Heart_Naproxen_Exp2_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Naproxen

value: CGGAACTG-TCGTAGTG


title: gastrocnemius muscle from 18 months-old Pex-KO mice, KO_070

description: Transcriptome profile of Pex5 knockout KO, biological rep3

value: gastrocnemius muscle

value: 18 months-old


title: KO liver rep2

description: Library name: Unknown_CL748-001T0017

value: liver


title: Heart, Naproxen, Experimental batch 2, Rep 06

description:
Library name: Heart_Naproxen_Exp2_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: CATAATAC-CGTTAGAA


title: TSC44

tag: nationality

value: Japanese


title: gastrocnemius muscle from 18 months-old Pex-KO mice, KO_063

description: Transcriptome profile of Pex5 knockout KO, biological rep2

tag: tissue


title: Heart, Naproxen, Experimental batch 2, Rep 01

description:
Library name: Heart_Naproxen_Exp2_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: Sex

value: 11 weeks

value: CCATTCGA-CGGACAAC


title: KO tumorliver rep2

description: Library name: Unknown_CL748-001T0011

source_name: liver tissue adjacent to metastases

value: liver tissue adjacent to metastases


title: TSC43

value: male


title: gastrocnemius muscle from 18 months-old Pex-KO mice, KO_054

description: Transcriptome profile of Pex5 knockout KO, biological rep1


title: KO tumorliver rep1

description: Library name: Unknown_CL748-001T0010


title: Heart, Control, Experimental batch 2, Rep 07

description:
Library name: Heart_Control_Exp2_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Control

tag: experimental batch

value: PolyA

value: TGGCCGGT-GCGCTCTA


title: TSC42

value: female

value: child maltreatment


title: gastrocnemius muscle from 18 months-old control mice, WT_107

description: Transcriptome profile of control WT, biological rep7

value: wild type


title: Heart, Naproxen, Experimental batch 2, Rep 04

description:
Library name: Heart_Naproxen_Exp2_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

value: Naproxen

value: Illumina TruSeq Stranded mRNA library prep kit

tag: index barcode

value: ATTGTGAA-GCAATGCA


title: WT tumorliver rep3

description: Library name: Unknown_CL748-001T0009


title: TSC41

value: buccal epithelial

value: typically developing


title: gastrocnemius muscle from 18 months-old control mice, WT_106

description: Transcriptome profile of control WT, biological rep6

value: gastrocnemius muscle

value: 18 months-old


title: Heart, Control, Experimental batch 2, Rep 06

description:
Library name: Heart_Control_Exp2_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: 11 weeks

tag: animal id

value: CCTTCACC-GGAGCGTC


title: WT tumorliver rep2

description: Library name: Unknown_CL748-001T0008

value: liver tissue adjacent to metastases


title: WT liver rep1

description: Library name: Unknown_CL748-001T0013

value: liver


title: TSC40

value: Japanese


title: Heart, Control, Experimental batch 2, Rep 05

description:
Library name: Heart_Control_Exp2_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Control

tag: dissection batch

value: PolyA

value: ACACTAAG-ATATGGAT


title: Heart, Control, Experimental batch 2, Rep 04

description:
Library name: Heart_Control_Exp2_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

value: TAAGGTCA-CTACGACA


title: KO tumorliver rep3

description: Library name: Unknown_CL748-001T0012

tag: genotype


title: gastrocnemius muscle from 18 months-old control mice, WT_102

description: Transcriptome profile of control WT, biological rep4

value: wild type


title: TSC38

value: male

value: child maltreatment


title: KO tumor rep3

description: Library name: Unknown_CL748-001T0006

source_name: metastases

value: metastases


title: Heart, Control, Experimental batch 2, Rep 03

description:
Library name: Heart_Control_Exp2_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Illumina TruSeq Stranded mRNA library prep kit

value: GATCTATC-AGCCTCAT


title: gastrocnemius muscle from 18 months-old control mice, WT_078

description: Transcriptome profile of control WT, biological rep3

value: gastrocnemius muscle

value: 18 months-old


title: Heart, Control, Experimental batch 2, Rep 08

description:
Library name: Heart_Control_Exp2_08
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: 11 weeks

value: GAATGAGA-AATGCCTC


title: gastrocnemius muscle from 18 months-old control mice, WT_104

description: Transcriptome profile of control WT, biological rep5


title: Heart, Control, Experimental batch 2, Rep 02

description:
Library name: Heart_Control_Exp2_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: CAACAATG-CCGTGAAG


title: TSC39

value: buccal epithelial

value: typically developing

value: Japanese


title: WT tumorliver rep1

description: Library name: Unknown_CL748-001T0007

value: liver tissue adjacent to metastases


title: KO tumor rep2

description: Library name: Unknown_CL748-001T0005


title: Heart, Control, Experimental batch 2, Rep 01

description:
Library name: Heart_Control_Exp2_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

value: Control

value: PolyA

value: ACTCGTGT-GTTCCAAT


title: gastrocnemius muscle from 18 months-old control mice, WT_077

description: Transcriptome profile of control WT, biological rep2

value: wild type


title: KO tumor rep1

description: Library name: Unknown_CL748-001T0004

value: metastases


title: WT tumor rep3

description: Library name: Unknown_CL748-001T0003


title: TSC36

value: female

value: child maltreatment


title: Heart, Naproxen, Experimental batch 1, Rep 10

description:
Library name: Heart_Naproxen_Exp1_10
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Naproxen

value: Male

value: Illumina TruSeq Stranded mRNA library prep kit

value: GCACGGAC-TGCGAGAC


title: gastrocnemius muscle from 9 months-old Pex-KO mice, KO_36

description: Transcriptome profile of Pex5 knockout KO, biological rep7

extract_protocol:
Total RNA was extracted from gastrocnemius muscle using TRIzol reagent (Life Technologies) following manufacturer's protocol
the QuantSeq 3' mRNA-seq Library Prep kit (Lexogen) was employed for library construction following manufacturer's protocol

treatment_protocol: Muscle-specific Pex5 ablation was achieved by crossing Pex5 floxed mice  with a transgenic line expressing Cre recombinase (CRE) under the control of Myosin Light Chain 1 fast promoter. Gastrocnemius muscle from 9 months-old mice was collected.

value: gastrocnemius muscle

value: 9 months-old


title: TSC35

value: buccal epithelial

value: typically developing


title: TSC34

value: male

value: Japanese


title: WT tumor rep2

description: Library name: Unknown_CL748-001T0002


title: gastrocnemius muscle from 9 months-old Pex-KO mice, KO_32

description: Transcriptome profile of Pex5 knockout KO, biological rep6


title: Heart, Naproxen, Experimental batch 1, Rep 09

description:
Library name: Heart_Naproxen_Exp1_09
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

extract_protocol:
At the end of the treatment period, mice were sacrificed via CO2 asphyxiation and their whole heart and jejunum tissue were dissected, chopped into small pieces, and snap frozen in liquid nitrogen. Jejuna were flushed with PBS to remove fecal matter prior to chopping and freezing. RNA was extracted from whole heart or 30 mg of jejunum using the Promega Maxwell RSC simplyRNA Tissue Kit (AS1340).
Libraries for each sample were constructed from 400 ng of total RNA using either the Illumina TruSeq Stranded mRNA library prep kit (heart) or the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (jejunum). Jejuna RNA samples were processed with a ribo-depletion based library prep kit because they had RIN scores < 8.

value: Heart

value: 11 weeks

value: AAGTCCAA-TACTCATA


title: WT tumor rep1

description: Library name: Unknown_CL748-001T0001


title: gastrocnemius muscle from 9 months-old Pex-KO mice, KO_26

description: Transcriptome profile of Pex5 knockout KO, biological rep5


title: TSC33


title: Heart, Naproxen, Experimental batch 1, Rep 07

description:
Library name: Heart_Naproxen_Exp1_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: PolyA

value: CTCTCGTC-AGGTTATA